[gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)

[Gerrit Groenhof]

Are you trying to run with more than one thread?
If so, try mdrun -nt 1 

Gerrit

> 
>   1. Re: gromacs QM/MM compilation with gaussian (Txema Mercero)
>   2. Re: Periodic Boundary Conditions g_mindist -pi (ifat shub)
>   3. Re: Re: Periodic Boundary Conditions g_mindist -pi (Mark Abraham)
> 
> 
> --
> 
> Message: 1
> Date: Wed, 16 Feb 2011 12:23:49 +0100
> From: Txema Mercero 
> Subject: [gmx-users] Re: gromacs QM/MM compilation with gaussian
> To: gmx-users@gromacs.org
> Cc: Edu Ogando , Jon I?aki Mujika
>   
> Message-ID:
>   
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi there!
> 
> We are trying to compile gromacs with Gaussian 03 rev D.02 (we also
> have g09). We followed the instructions in
> http://wwwuser.gwdg.de/~ggroenh/roadmap.pdf despite that they do no
> fit exactly  with the g03 rev d03 version,for instance, FrcNCN is no
> in l710 but in utilam.F
> 
> Despite of that, we compiled gromacs and  apparently everything was
> fine, but we get a segmentation fault when we run gromacs. We have the
> following questions
> 
> 1.- Is it possible to get a more detailed/or specific instructions?
> 2.- I think that three variables GAUSS_EXE, GAUSS_DIR and DEVEL_DIR
> should be defined. Where should GAUSS_EXE and GAUSS_DIR point exactly?
> 
> Thanks for your attention, any help will be appreciated.
> 
> Regards,
> 
> Txema Mercero
> IZO/SGI
> UPV/EHU
> 
> 
> --
> 
> Message: 2
> Date: Wed, 16 Feb 2011 13:30:29 +0200
> From: ifat shub 
> Subject: [gmx-users] Re: Periodic Boundary Conditions g_mindist -pi
> To: gmx-users@gromacs.org
> Message-ID:
>   
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi Tsjerk,
> Thank you for your reply.
> I am aware of the trajconv option but I wanted to know if there is a way to
> avoid these kind of jumps over the periodic boundaries during the mdrun and
> not post process?
> Thanks,
> Ifat
> 
> message: 4
>> Date: Wed, 16 Feb 2011 11:19:14 +0200
>> From: ifat shub 
>> Subject: [gmx-users] Periodic Boundary Conditions g_mindist -pi
>> To: gmx-users@gromacs.org
>> Message-ID:
>>   
>> Content-Type: text/plain; charset="iso-8859-1"
>> 
>> Hi,
>> 
>> 
>> 
>> I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see
>> if the complex is seeing its next periodic image, so I used the g_mindist
>> command with the -pi option. My command line was:
>> 
>> g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi
>> 
>> The output (see below) was stable until ~344ps when there is a  jump in the
>> max internal distance (third column) from ~6nm to ~22nm. After the jump the
>> numbers are reduced back to ~6nm and remained stable until the run is
>> completed at 1ns.
>> 
>> Does anyone know how to explain this jump? Is this a real problem or just a
>> visualization artifact? Is there a way to avoid such jumps?
>> 
>> 
>> 
>> Here is the mdp file I used:
>> 
>> --run.mdp--
>> 
>> integrator  = md
>> 
>> nsteps  = 100
>> 
>> dt  = 0.001
>> 
>> coulombtype = pme
>> 
>> vdw-type= cut-off
>> 
>> tcoupl  = Berendsen
>> 
>> tc-grps = protein non-protein
>> 
>> tau-t   = 0.1 0.1
>> 
>> ref-t   = 310 310
>> 
>> nstxout = 100
>> 
>> nstvout = 0
>> 
>> nstxtcout   = 100
>> 
>> nstenergy   = 100
>> 
>> comm_mode = Linear ; Angular
>> 
>> comm_grps= Protein
>> 
>> xtc_grps   = Protein
>> 
>> energygrps = Protein
>> 
>> --
>> 
>> 
>> 
>> Thanks,
>> 
>> Ifat
>> 
>> 
>> 
>> The output:
>> 
>> 343.7   10.813 5.924   16.445 16.445 16.445
>> 
>> 343.8   10.809 5.949   16.445 16.445 16.445
>> 
>> 343.9   10.804 5.959   16.445 16.445 16.445
>> 
>> 344  10.808 5.974   16.445 16.445 16.445
>> 
>> 344.1   0.18 21.982 16.445 16.445 16.445
>> 
>> 344.2   10.778 5.977   16.445 16.445 16.445
>> 
>> 344.3   10.768 5.996   16.445 16.445 16.445
>> 
>> 344.4   10.764 6.016   16.445 16.445 16.445
>> 
>> 344.5   10.722 6.029   16.445 16.445 16.445
>> 
>> 344.6   10.774 6.01 16.445 16.445 16.445
>> 
>> 344.7   0.174   21.984 16.445 16.445 16.445
>> 
>> 344.8   0.176   21.98   16.445 16.445 16.445
>> 
>> 344.9   0.17 22.002 16.445 16.445 16.445
>> 
>> 345  0.173   21.981 16.445 16.445 16.445
>> 
>> 345.1   0.191   21.954 16.445 16.445 16.445
>> 
>> 345.2   0.183   21.958 16.445 16.445 16.445
>> 
>> 345.3   0.181   22.012 16.445 16.445 16.445
>> 
>> 345.4   0.17 22.054 16.445 16.445 16.445
>> 
>> 345.5   0.168   22.054 16.445 16.445 16.445
>> 
>> 345.6   0.189   22.039 16.445 16.445 16.445
>> 
>> 345.7   0.171   22.007 16.445 16.445 16.445
>> 
>> 345.8   0.186   22.031 16.445 16.445 16.445
>> 
>> 345.9   0.171   22.077 16.445 16.445 16.445
>> 
>> 346  0.187   21.99   16.445 16.445 16.445
>> 
>> 346.1   0.173   21.984 16.445 16.445 16.445
>> 
>> 346.2   0.181   22.02   16.445 16.445 16.445
>> 
>> 

Re: [gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)

[Gerrit Groenhof]

/libxml2.so.2.6.26
> 3de4733000-3de473c000 rw-p 00133000 08:02 10310609
>  /usr/lib64/libxml2.so.2.6.26
> 3de473c000-3de473d000 rw-p 3de473c000 00:00 0
> 3dea20-3dea20d000 r-xp  08:02 5751072
>  /lib64/libgcc_s-4.1.2-20080825.so.1
> 3dea20d000-3dea40d000 ---p d000 08:02 5751072
>  /lib64/libgcc_s-4.1.2-20080825.so.1
> 3dea40d000-3dea40e000 rw-p d000 08:02 5751072
>  /lib64/libgcc_s-4.1.2-20080825.so.1
> 2b0e5affe000-2b0e5b00 rw-p 2b0e5affe000 00:00 0
> 2b0e5b00-2b0e5b07e000 r-xp  00:18 20054237
>  /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmxpreprocess.so.6.0.0
> 2b0e5b07e000-2b0e5b27d000 ---p 0007e000 00:18 20054237
>  /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmxpreprocess.so.6.0.0
> 2b0e5b27d000-2b0e5b28 rw-p 0007d000 00:18 20054237
>  /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmxpreprocess.so.6.0.0
> 2b0e5b28-2b0e5b2ae000 rw-p 2b0e5b28 00:00 0
> 2b0e5b2ae000-2b0e5b3b9000 r-xp  00:18 20054231
>  /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6.0.0
> 2b0e5b3b9000-2b0e5b5b9000 ---p 0010b000 00:18 20054231
>  /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6.0.0
> 2b0e5b5b9000-2b0e5b5bc000 rw-p 0010b000 00:18 20054231
>  /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6.0.0
> 2b0e5b5bc000-2b0e5b5bd000 rw-p 2b0e5b5bc000 00:00 0
> 2b0e5b5bd000-2b0e5b74c000 r-xp  00:18 49184804
>  /software/fftw-3.2.2_intel_11.0.069/lib/libfftw3f.so.3.2.4
> 2b0e5b74c000-2b0e5b94b000 ---p 0018f000 00:18 49184804
>  /software/fftw-3.2.2_intel_11.0.069/lib/libfftw3f.so.3.2.4
> 2b0e5b94b000-2b0e5b958000 rw-p 0018e000 00:18 49184804
>  /software/fftw-3.2.2_intel_11.0.069/lib/libfftw3f.so.3.2.4
> 2b0e5b958000-2b0e5b959000 rw-p 2b0e5b958000 00:00 0
> 2b0e5b96d000-2b0e5b96e000 rw-p 2b0e5b96d000 00:00 0
> 2b0e5b96e000-2b0e5000 r-xp  00:18 20054224
>  /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmx.so.6.0.0
> 2b0e5000-2b0e5bdbb000 ---p 0024d000 00:18 20054224
>  /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmx.so.6.0.0
> 2b0e5bdbb000-2b0e5bdcd000 rw-p 0024d000 00:18 20054224
>  /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmx.so.6.0.0
> 2b0e5bdcd000-2b0e5bdce000 rw-p 2b0e5bdcd000 00:00 0
> 2b0e5bdce000-2b0e5c0b7000 r-xp  00:17 6031605
>  /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.so
> 2b0e5c0b7000-2b0e5c1b6000 ---p 002e9000 00:17 6031605
>  /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.so
> 2b0e5c1b6000-2b0e5c1c1000 rw-p 002e8000 00:17 6031605
>  /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.so
> 2b0e5c1c1000-2b0e5c1c9000 rw-p 2b0e5c1c1000 00:00 0
> 2b0e5c1c9000-2b0e5c8c6000 r-xp  00:17 6031615
>  /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so
> 2b0e5c8c6000-2b0e5c9c6000 ---p 006fd000 00:17 6031615
>  /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so
> 2b0e5c9c6000-2b0e5c9d2000 rw-p 006fd000 00:17 6031615
>  /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so
> 2b0e5c9d2000-2b0e5c9dd000 rw-p 2b0e5c9d2000 00:00 0
> 2b0e5c9dd000-2b0e5cc7a000 r-xp  00:17 6031599
>  /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so
> 2b0e5cc7a000-2b0e5cd7a000 ---p 0029d000 00:17 6031599
>  /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so
> 2b0e5cd7a000-2b0e5cd7f000 rw-p 0029d000 00:17 6031599
>  /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so
> 2b0e5cd7f000-2b0e5cd92000 rw-p 2b0e5cd7f000 00:00 0
> 2b0e5cd92000-2b0e5cfe2000 r-xp  00:17 6783119
>  /opt/intel/Compiler/11.1/073/lib/intel64/libimf.so
> 2b0e5cfe2000-2b0e5d0e1000 ---p 0025 00:17 6783119
>  /opt/intel/Compiler/11.1/073/lib/intel64/libimf.so
> 2b0e5d0e1000-2b0e5d126000 rw-p 0024f000 00:17 6783119
>  /opt/intel/Compiler/11.1/073/lib/intel64/libimf.so
> 2b0e5d126000-2b0e5d23c000 r-xp  00:17 6783139
>  /opt/intel/Compiler/11.1/073/lib/intel64/libsvml.so
> 2b0e5d23c000-2b0e5d33b000 ---p 00116000 00:17 6783139
>  /opt/intel/Compiler/11.1/073/lib/intel64/libsvml.so
> 2b0e5d33b000-2b0e5d33c000 rw-p 00115000 00:17 6783139
>  /opt/intel/Compiler/11.1/073/lib/intel64/libsvml.so
> 2b0e5d33c000-2b0e5d377000 r-xp  00:17 6783121
>  /opt/intel/Compiler/11.1/073/lib/intel64/libintlc.so.5
> 2b0e5d377000-2b0e5d476000 ---p 0003b000 00:17 6783121
>  /opt/intel/Compiler/11.1/073/lib/intel64/libintlc.so.5
> 2b0e5d476000-2b0e5d479000 rw-p 0003a000 00:17 6783121
>  /opt/intel/Compiler/11.1/073/lib/intel64/libintlc.so.5
> 2b0e5d479000-2b0e5d8b9000 rw-p 2b0e5d479000 00:00 0
> 2b0e6000-2b0e60021000 rw-p 2b0e6000 00:00 0
> 2b0e60021000-2b0e6400 ---p 2b0e60021000 00:00 0
> 7fff4fa96000-7fff4faaa000 rwxp 7ff

[gmx-users] R. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero)

[Gerrit Groenhof]

>   2. Re: Re: gromacs QM/MM compilation with gaussian (Txema
>  Mercero) (Txema Mercero)

Can you send me your tpr file? 

Gerrit

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Re: [gmx-users] R. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero)

[Gerrit Groenhof]

 Hi,

With gmx 5.5.3 your input works here. Still it crashes in g09, but that 
is because you have a multiplicity of 1 with 181 electrons.


QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 24
QMlevel: RHF/6-31G

number of CPUs for gaussian = 1
memory for gaussian = 5000
accuracy in l510 = 8
NOT using cp-mcscf in l1003
Level of SA at start = 0
/home/ggroenh/g09/gaussian initialised...

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+02
   Number of steps= 1000
Calling '/home/ggroenh/g09//g09 < input.com > input.log'

---
Program mdrun, VERSION 4.5.3
Source code file: qm_gaussian.c, line: 913

Fatal error:
Call to '/home/ggroenh/g09//g09 < input.com > input.log' failed

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"I Used To Care, But Things Have Changed" (Bob Dylan)

On 02/17/2011 10:39 AM, Txema Mercero wrote:

Here it goes.

On Thu, Feb 17, 2011 at 9:49 AM, Gerrit Groenhof  wrote:

   2. Re: Re: gromacs QM/MM compilation with gaussian (Txema
  Mercero) (Txema Mercero)

Can you send me your tpr file?

Gerrit

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[gmx-users] Re: gmx-users Digest, Vol 82, Issue 189

[Gerrit Groenhof]

Since this is a gaussian related question why do you ask it at the gromacs user 
list? 

Anyway, the problem you have is that you have inserted a space between the 6-31 
and G in the basisset specification. Gaussian has been kind enough to tell you 
this (see the ' in the second line of the error).

Gerrit


On 24 Feb 2011, at 20:10, gmx-users-requ...@gromacs.org wrote:

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> Today's Topics:
> 
>   1. GAUSSIAN Error message (Sergio Manzetti)
>   2. Re: GAUSSIAN Error message (TJ Mustard)
>   3. Re: GAUSSIAN Error message (Sergio Manzetti)
> 
> 
> --
> 
> Message: 1
> Date: Fri, 25 Feb 2011 02:29:42 +0800
> From: Sergio Manzetti 
> Subject: [gmx-users] GAUSSIAN Error message
> To: Discussion list for GROMACS users 
> Message-ID:
>   
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hello, I am getting an unknown error message in the submission of the G03
> file:
> 
>  QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE.
> # HF/6-31G OPT FREQ ^M ^M ARGUSLAB-GENERAT
> '
> Last state="GCL"
> TCursr=  909 LCursr=   20
> Error termination via Lnk1e in Gaussian64/g03/l1.exe at Thu Feb 24 19:26:31
> 2011.
> Job cpu time:  0 days  0 hours  0 minutes  0.1 seconds.
> File lengths (MBytes):  RWF=  9 Int=  0 D2E=  0 Chk=  1
> Scr=  1
> 
> 
> The submission file is prepared in Argus Lab and looks as follows:
> 
> %chk=BuckyBall.chk
> # HF/6-31G Opt Freq
> 
> ArgusLab-generated input file for BuckyBall
> 
> 0  3
> C-0.677394-0.928398-3.166238
> C0.672998-0.928446-3.166308
> C1.0902870.355662-3.166349
> C-0.0022521.149252-3.166236
> C-1.0947610.355692-3.166308
> C-2.2073000.717126-2.443529
> C-1.364869-1.874482-2.443334
> C1.360544-1.874612-2.443455
> C2.2027690.717064-2.443539
> C-0.0022732.318671-2.443310
> C2.453119-1.519766-1.733636
> C2.878066-0.212169-1.733664
> C2.2026961.865587-1.733573
> C1.0901852.673574-1.733478
> C-1.0947502.673602-1.733477
> C-2.2072941.865663-1.733587
> C-2.882593-0.212075-1.733651
> C-2.457472-1.519622-1.733552
> C-0.689644-2.803573-1.733436
> C0.685341-2.803673-1.733490
> C-1.364814-3.022879-0.584899
> C-2.457440-2.229447-0.584919
> C1.360538-3.023080-0.584938
> C2.453142-2.229641-0.584965
> C3.2954420.362133-0.584991
> C2.8779911.646286-0.584972
> C0.6728813.247762-0.584900
> C-0.6774413.247772-0.584900
> C-2.8826691.646412-0.584987
> C-3.3001250.362235-0.584997
> C-0.677324-3.2462440.584596
> C0.673012-3.2463560.584600
> C2.878165-1.6449290.584675
> C3.295525-0.3607300.584685
> C2.4530282.2310400.584637
> C1.3604223.0245220.584617
> C-2.4576442.2311330.584645
> C-1.3649783.0245500.584620
> C-2.882566-1.6447980.584681
> C-3.300136-0.3606380.584699
> C1.090333-2.6722231.733208
> C2.202882-1.8642451.733311
> C-2.207252-1.8641231.733266
> C-1.094677-2.6721151.733166
> C-2.8827100.2136741.733376
> C-2.4576671.5212871.733309
> C-0.6897782.8052321.733169
> C0.6852562.8052261.733176
> C2.8781580.2135981.733360
> C2.4531091.5212171.733301
> C-0.002190-2.3172212.442969
> C-2.207307-0.7155702.443173
> C-1.3649941.8761052.443040
> C1.3604901.8760862.443059
> C2.202875-0.7156462.443217
> C-0.6774280.9299253.165780
> C0.6729580.9299153.165806
> C1.090307-0.3541913.165883
> C-0.002209-1.1477443.165767
> C-1.094738-0.3541563.165831
> Gd-0.0048700.001706-0.000166
> 
> --Link1--
> %chk=BuckyBall.chk
> # HF/6-31G Opt FreqCube=(orbitals)
> Geom=AllCheck Guess=(Read,Only)
> 
> BuckyBall_orbitals.cub
>  212   213
> 
> --Link1--
> %chk=BuckyBall.chk
> # HF/6-31G Opt FreqCube=(density)
> Geom=AllCheck Guess=(Read,Only)
> 
> BuckyBall_density.cub
> 
> --Link1--
> %chk=BuckyBall.chk
> # HF/6-31G Opt FreqCube=(spin)
> Geom=AllCheck Guess=(Read,Only)
> 
> BuckyBall_spin

[gmx-users] Re: 4. Re: QMMM (Txema Mercero)

[Gerrit Groenhof]

 Please be more specific than not successful.

And also please understand that there are two things involved: the 
installation, which is so complicated because the gaussian license 
forbids distrubution of source code.


The actual QM, which sometimes is not thought through well enough. A 
general advice therefore is to first try to see if you can do the QM on 
the isolated (sub) system with a default QM package.


Since the interface with Orca runs and installs more smoothly, I suggest 
try that.


Hope this helps,

Gerrit



4. Re: QMMM (Txema Mercero)


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[gmx-users] Re: gmx-users Digest, Vol 83, Issue 63

[Gerrit Groenhof]

 The choice for the QM package depends on what level of QM theory you 
wish to use and what package are available to you. to proceed sue the 
instructions http://wwwuser.gwdg.de/~ggroenh/qmmm.html


Be aware though that QMMM is not to be considered a black box method.

Gerrit



4. QMMM (Haresh)

\

Respected sir,

I am new user in gromacs.
I want to run QMMM on gromacs.
Should I have install all source code like mopac7, guessin,gamess-UK  for QMMM ?

Please help me out.

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[gmx-users] Re: Parameterization of a molecule containing a radical, (oxygen) (Justin A. Lemkul)

[Gerrit Groenhof]

There is a AMBER FF for this kind of nitroxide spin labels. See PCCP 12 
(2010) 11697.



Hope it helps,

Gerrit

Simone Cirri wrote:

Hi all,
I have a question regarding a new parameterization: actually, I'm
wondering whether or not it is possible to do it.

The molecule is tempol; you cand find its PubChem entry
here http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=137994&loc=ec_rcs

As you can see, the problem of this molecule is its O radical; this, and
the N belonging to the cycle too.
My lab would really benefit from the parameterization (for the AMBER
force field) of tempol, since we commonly use it in our NMR experiments.
We don't know how to treat the oxygen radical and the N bound to it, though.
If this parameterization is impossible to do we will give up, but we
would like to be sure about it.
Thanks in advance for any answer you could provide.


This would not be a trivial molecule to parameterize.  You could start by using
antechamber (available free as part of AmberTools), since it allows you to tune
multiplicity (-m flag).  Otherwise, the existing force fields may not provide a
suitable atom type for the O radical or its effects on the rest of the molecule.
   I still don't know if parameterization would be possible for a standard MM
force field (though it very well might), but this might get you started.



-Justin


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[gmx-users] Re: gmx-users Digest, Vol 84, Issue 177

[Gerrit Groenhof]

> 
>   4. PYP Connection (Taylor Kaplan)


Are the connections between the chromophore and cysteine there? You can check 
this by scanning your topology file for the indices of the sulphur and C1 atom 
in the [ bonds ] section. 

You can use the specbond the attach the chromophore to the protein. THis so far 
always worked for us.

hope it helps,

Gerrit



> Message: 4
> Date: Thu, 21 Apr 2011 00:48:07 -0700 (PDT)
> From: Taylor Kaplan 
> Subject: [gmx-users] PYP Connection
> To: Discussion list for GROMACS users 
> Message-ID: <441414.8442...@web36601.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi Rama,
> 
>I was looking at the tdb files for the amber03 force field ( I didn't 
> change anything, i just read with the cat command ), anyways I didn't see 
> anything written in the tdb -n or -c terminal files. After reading the 
> gromacs manual on topology files, it said that residue connection types and 
> such are specified through the tdb file. I'm only guessing that since the 
> chromophore isn't an amino acid that it may have a different connection 
> deviating from the traditional -n or -c terminals. So I was wondering if the 
> amber force field was using the .tdb files that comes standard with gromacs 
> ,... which I'm pretty sure lacks the type of connection that pyp makes with 
> the protein. So to fix this problem, do we need to make or modify the .tdb 
> file for the chromophore, or is the .tdb file of no concern? 
> 
> Thanks,
> 
> Taylor
> 
> --- On Wed, 4/20/11, Ramachandran G  wrote:
> 
> From: Ramachandran G 
> Subject: Re: [gmx-users] PYP chromophore force field
> To: "Peter C. Lai" 
> Cc: "gmx-users@gromacs.org" 
> Date: Wednesday, April 20, 2011, 5:12 PM
> 
> 
> Yes, you are right, the chromophore(p-coumaric acid) is covalently bonded to 
> the Sulphur(S) atom of the Cys-69 residue.
> But I specified the covalent bond in my topology.
> 
> [ bonds]
>  C   +SG
> 
> [ angles ]
> 
>   OC   +SG   
>  CA1   C   +SG   
>   C  +SG   +CB  
> 
> [ dihedrals ]
>   O C  +SG+CB
>  CA1C  +SG+CB
>  HA2   CA1   C   +SG
>  CA2   CA1   C   +SG
>   C   +SG  +CB   +CA
> 
>   C   +SG  +CB   +HB1
>   C   +SG  +CB   +HB2
> 
> After doing pdb2gmx, i got the right structure. But the chromophore flies 
> away after minimising. 
> 
> 
> Thanks
> Rama
> 
> On Wed, Apr 20, 2011 at 4:57 PM, Peter C. Lai  wrote:
> 
> Isn't the chromophore supposed to be covalently bonded to the protein?
> 
> My cursory search shows Vengris et al 2004 in Biophys. J. citing Baca et al
> 
> 1994 and van Beeumen et al 1993: "This small 125-residue protein contains a
> 
> p-coumaric acid chromophore that is covalently bound to the protein backbone
> 
> via a thiol-ester cysteine linkage Cys-69"...
> 
> 
> 
> Maybe you forgot to specify a covalent bond in your topology...
> 
> 
> 
> On 2011-04-20 06:46:54PM -0500, Ramachandran G wrote:
> 
>> Hi gromacs users,
> 
>>  I am working on Photo active yellow protein.
> 
>> 
> 
>> Although i successfully build the force field and patched the 
>> chromophore to the protein.
> 
>> After energy minimizing the protein, the chromophore flies away separately. 
>> I don't know whether i am missing anything?
> 
>> Please help.
> 
>> Rama
> 
>> 
> 
>> 
> 
> 
> 
>> --
> 
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> 
> 
> 
> 
> 
> --
> 
> ===
> 
> Peter C. Lai | University of Alabama-Birmingham
> 
> Programmer/Analyst   | BEC 257
> 
> Genetics, Div. of Research   | 1150 10th Avenue South
> 
> p...@uab.edu  | Birmingham AL 35294-4461
> 
> (205) 690-0808   |
> 
> ===
> 
> 
> 
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> 
> 
> 
> 
> 
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[gmx-users] Re:qmmm temp definition + linking atom

[Gerrit Groenhof]

 The link atom can be placed anywhere at step 0. These atom are treated 
like virtual sites and will thus be placed at the defined position along 
the QM/MM bond that  needs capping.


Concerning the temperature, one can treat the QM atoms as a separate 
group indeed. But as Mark said, why not expose the whole system to the 
temp-shock?


Gerrit




4. qmmm temp definition (Yao Yao)
5. qmmm linking atom (Yao Yao)
6. Re: qmmm temp definition (Mark Abraham)


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[gmx-users] Re: gmx-users Digest, Vol 85, Issue 114

[Gerrit Groenhof]

> 
>   3. QMMM+NMA (Yao Yao)
>   
> Hi Gmxers,
> 
> I am wondering if NMA has been introduced into QMMM part of gromacs.
> I am trying to get vibrational frequencies of proteins by normal mode 
> analysis (NMA) in the framework of QMMM.

This is not possible, unless your system is so small that you can evaluate the 
hessian numerically.

Gerrit


> 
> Thanks,
> 
> Yao 
> 
> va...@gmail.com>
> Subject: Re: [gmx-users] about side chain and structure rifinement
> To: Discussion list for GROMACS users 
> Message-ID: 
> Content-Type: text/plain; charset="iso-8859-1"
> 
> A MM ff like OPLS will probably do your job. However CASP experiments show
> that knowledge-based potentials like the one Rosetta implements, produce
> more physically realistic results. If you only want to improve the
> side-chain conformations, I'd suggest to use a program that employs rotamer
> libraries like SCWRL4.
> 
> 
> On 17 May 2011 12:05, marco miele  wrote:
> 
>> Hi everyone
>> My question is that I have a receptor protein modeled which have some
>> problem with side chain angles, I would like to know if is good to
>> apply OPLS ff in vacuum to improve the side chain in particularly and
>> structure in general.
>> what you suggest me.
>> Cheer marco
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>> 
> 
> 
> 
> -- 
> 
> ==
> 
> Thomas Evangelidis
> 
> PhD student
> 
> Biomedical Research Foundation, Academy of Athens
> 
> 4 Soranou Ephessiou , 115 27 Athens, Greece
> 
> email: tev...@bioacademy.gr
> 
>  teva...@gmail.com
> 
> 
> website: https://sites.google.com/site/thomasevangelidishomepage/
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[gmx-users] Re: on MD at constant pH (Acoot Brett)

[Gerrit Groenhof]

You could have a look at 
Donnini et al, JCTC 7 (2011), 1962-1978
And with teh code available from 
http://www.mpibpc.mpg.de/home/grubmueller/projects/Methods/ConstpH/index.html
give it a try for your problem.

Gerrit

> 
>   1. on MD at constant pH (Acoot Brett)
>
> 
> Dear All,
> 
> Currently is it possible to run MD at a constant pH value?
> 
> I am looking forward to getting a reply from you.
> 
> Cheers,
> 
> Acoot
> -
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[gmx-users] 4. QM/MM Calculation with Orca (Minos Matsoukas)

[Gerrit Groenhof]

YOucan only use one thread in mdrun, but more than one in ORCA. Try to estimate 
the ratio of computation time spent between the QM and MM calculation to get an 
idea of why we never bothered to parallellize the MM part.

Hope this helps,

Gerrit


> 
>   4. QM/MM Calculation with Orca (Minos Matsoukas)
>   
> 
> Dear GROMACS Users,
> 
> I am using Gromacs with ORCA for a qm calculation, but I can only use
> 1 processor for mdrun.
> 
> If I place the line !PAL4 in the topol.ORCAINFO and run mdrun -nt 1,
> it works, and ORCA parallelizes correctly for 4 processors, although
> mdrun only runs one thread.
> 
> If I place the line !PAL4 in the topol.ORCAINFO and run mdrun -nt 4,
> it doesn‚t work. mdrun crashes with a segmentation fault error :
> 
> Back Off! I just backed up md.log to ./#md.log.35#
> Reading file topol.tpr, VERSION 4.5.5 (single precision)
> Starting 4 threads
> QM/MM calculation requested.
> QM/MM calculation requested.
> QM/MM calculation requested.
> QM/MM calculation requested.
> there we go!
> there we go!
> there we go!
> there we go!
> Layer 0
> nr of QM atoms 73
> QMlevel: B3LYP/STO-3G
> 
> /opt/soft/orca_2_9_1_linux_x86-64/opt/soft/orca_2_9_1_linux_x86-64...
> orca initialised...
> Segmentation fault (core dumped)
> 
> 
> Is this because mdrun can only run with 1 thread when used with ORCA ?
> 
> Here‚s some information :
> OS: CentOS 6.2 x86_64 kernel 2.6.32-220
> GROMACS: 4.5.5 compiled with options : --with-qmmm-orca 
> --without-qmmm-gaussian
> ORCA: 2.9.1 for x86_64
> OPENMPI: 1.4.3
> 
> My minimization mdp file is:
> 
> ;
> ; Input file
> ;
> title   =  Yo ; a string
> cpp =  /lib/cpp   ; c-preprocessor
> integrator  =  cg ;
> ;integrator   = l-bfgs
> 
> rlist   =  1.0; cut-off for ns
> rvdw=  1.0; cut-off for vdw
> rcoulomb=  1.5; cut-off for coulomb
> ;   Energy minimizing stuff
> ;
> nsteps  =  200
> emtol   =  10
> emstep  =  0.1
> ;define  = -DPOSRES
> constraints = none
> QMMM = yes
> QMMM-grps= MOL
> QMMMscheme   = normal
> QMbasis  = STO-3g
> QMmethod = b3lyp
> QMcharge = 1
> QMmult   = 1
> -
> 
> Thanks in advance

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Re: [gmx-users] qmmm and "real-life" meaning of null

[Gerrit Groenhof]

Hi,

INdeed, you would still need a LJ term for the QM atoms, in order to interact 
with the MM atoms. Only if the radius around your special atom were larger than 
the LJ cut-off could you safely ignore the LJ paramter.

gerrit

> 
> Message: 3
> Date: Thu, 07 Jun 2012 19:47:02 -0400
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] qmmm and "real-life" meaning of null
>   lennard-jones   parameters
> To: Discussion list for GROMACS users 
> Message-ID: <4fd13d76.9040...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> 
> On 6/7/12 7:28 PM, Edward Deira wrote:
>> Dear all,
>> 
>> I'm currently starting to dwell deeper in MD, and I'm taking some time to
>> understand what's going on inside the gromacs "black-box".
>> In one of those dwellings, I came across an older post
>> [http://www.mail-archive.com/gmx-users@gromacs.org/msg42568.html] which 
>> reads:
>> 
>> Question:
>> 4. In ffnonbonded.itp, why are both sigma and epsilon set to zero for HW
>> (opls_117)? This seems to imply that, as far as Lennard-Jones interactions 
>> are
>> concerned, the hydrogens on the waters don't exist. Or, in other words, in 
>> the
>> absence of charges, the hydrogens don't "feel" the hydrogens, the hydrogens
>> don't "feel" the oxygens, and the oxygens don't "feel" the hydrogens. In 
>> other
>> words, the hydrogens interact with the world only via electrostatic 
>> (Coulombic)
>> interactions. Is this a correct interpretation?Correct. Many force fields do 
>> this.
>> Answer:
>> 
>> So, my question, if a question at all:
>> 
>> Suppose I have a regular protein and put inside some metal atom that will
>> coordinate with some O and N atoms from the side chains. If the sigma and
>> epsilon for that metal are null, than the metal - sidechains interactions are
>> exclusively electrostatic. Does this make sense ? What are the implications 
>> of
>> this for the "coordination chemistry" of that "metal - sidechain complex" ?
>> 
>> On the side: suppose I want some non parameterized metal atom, say W, for 
>> which
>> I will compute all the other parameters in the same/similar way described in 
>> the
>> force field papers, but for which no experimental data are available for me 
>> to
>> compare computable meaningful sigma and epsilon values. Can I just sigma and
>> epsilon to zero ? Or should I do qmmm to have W in the qm part ?
>> 
> 
> The fact that the LJ parameters for H are zero derives from its size.  The 
> environment is more strongly influenced by the heavy atom to which H is 
> bonded. 
>  In the case of a larger metal ion, I would seriously doubt that setting LJ 
> parameters to zero is valid.  It's quite convenient, but in most force 
> fields, 
> all metal ions have some LJ parameters.  Perhaps investigating how those 
> parameters were derived would be useful.  For what it's worth, I believe the 
> origin of the zero-LJ H parameters comes from this work:
> 
> http://pubs.acs.org/doi/abs/10.1021/ja00824a004
> 
>> Also, from the few tutorials and from the manual, I have the impression that
>> even for qmmm with gromacs and mopac i still need force field parameters for 
>> the
>> qm part, is this true ? Or i just need to include a qmmm section in all mdp
>> files, including the first ion adding and energy minimization steps ? Sorry 
>> for
>> the naivety in this, but i've only made "regular protein" MD so far.
>> 
> 
> I've never done any QM/MM, but my assumption would be that you have to have 
> some 
> valid topology to start with.  Perhaps someone else can comment on this 
> methodological issue.
> 
> -Justin
> 
> -- 
> 
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> 

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Antw: Re: Re: [gmx-users] constant PH simulations (Emanuel Peter)

[Gerrit Groenhof]

> 
>   2. Antw: Re: Re: [gmx-users] constant PH simulations (Emanuel Peter)
>   
> Message: 2
> Date: Tue, 06 Sep 2011 15:49:28 +0200
> From: "Emanuel Peter" 
> Subject: Antw: Re: Re: [gmx-users] constant PH simulations
> To: 
> Message-ID: <4e66410802f100014...@gwsmtp1.uni-regensburg.de>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> The standard procedure of H+ interchange and transition states can be done 
> through QM/MM.
> Please give one reference according to the algorithms you have mentioned.

Please check Donnini et al, JCTC 7 (2011), 1962-1978.and the references therein.

have a banana,

Gerrit

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Re: [gmx-users] constant PH simulations

[Gerrit Groenhof]

> 
> Message: 1
> Date: Wed, 07 Sep 2011 12:01:00 +0200
> From: "Emanuel Peter" 
> Subject: Antw: Re: Antw: Re: Re: [gmx-users] constant PH simulations
> To: 
> Message-ID: <4e675cfc02f100014...@gwsmtp1.uni-regensburg.de>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> At first I would like to say that I deeply apologize for 
> the cave-like things I have said. I again say, that this
> was not the field I am deeply involved.
>> From Gerrit I got a banana.
> For this guy, I am a cave-man.

No, a monkey, just like you signed one of your earlier mails.

The questions you raise are all unaswered, but extremely relevant. Futher open 
discussion is highly appreciated.


> 
> Generalized forces and averages for H+ interchange ?

The idea is that the protons are degrees of freedom. Protons can thus appear 
"spontaneously" on titrating sites. The driving force is the thermodynamic 
force: DG/Dl. More details can be foudn in the papers By Charly Brooks, JAna 
Khandogin and ourselves.

> Comparison with titration experiments ?

Not many of these around, but these will be crucial to establish the validty of 
the different approaches.

> Is there any experimental evidence for the rates of
> interchange ?

NMR maybe.

> Are simulation-times or the periods of interchange at 
> any time realistic?

Probably not.

> Are equilibria sampled well, with such interchanges,
> or are there jumps in free energy by this interchange ?

No the system follows the underlying free energy landscape always. THerefore 
there are no jumps, as one may habe in MC approaches. However, the price one 
pays is that one does sample intermediate state, in which the proton is only 
partially there.


> Why is there no free H+ ?

That would give an enormous sampling problem. Furthermore, the properties of MM 
hydroniom are very different from real hydronium

Hope this adds to the discussion.

Gerrit








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[gmx-users] Re 1. orca and qm/mm (xi zhao)

[Gerrit Groenhof]

Try to remove these lines, or put something there. The input is ignored, but 
since strings are used as input (for use in multui-layer oniom), leaving blank 
causes an error.

Gerrit
On 7 Nov 2011, at 14:21, gmx-users-requ...@gromacs.org wrote:

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>   1. orca and qm/mm (xi zhao)
> 
> 
> --
> 
> Message: 1
> Date: Mon, 7 Nov 2011 20:54:04 +0800 (CST)
> From: xi zhao 
> Subject: [gmx-users] orca and qm/mm
> To: gmx-users@gromacs.org
> Message-ID:
>   <1320670444.82465.yahoomailclas...@web15103.mail.cnb.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
> 
> All users:
> 
>  
> According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code, I want to build 
> qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, 
> ORCA_PATH and  BASENAME.ORCAINFO as told in the instruction. 
> BASENAME=pyp_qm
> here is the BASENAME.ORCAINFO file:
> ! RKS B3LYP/G SV(P) TightSCF Opt
>  
> here is the md file:
> integrator   = md
> tinit= 0
> dt   = 0.001
> nsteps   = 500
> nstcomm  = 1
> comm_grps= system
>  
> emtol= 100.0
> emstep   = 0.001
> nstcgsteep   = 50
>  
> nstxout  = 1
> nstvout  = 1
> nstfout  = 1
> nstlog   = 1
> nstenergy= 1
> nstxtcout= 1
> xtc_grps = system
> energygrps   = QMatoms rest_Protein SOL
>  
> nstlist  = 10
> ns_type  = grid
> pbc  = xyz
> rlist= 1.0
>  
> coulombtype  = cut-off
> rcoulomb = 1.4
> epsilon_r= 1
> vdwtype  = Cut-off
> rvdw = 1.4
>  
> tcoupl   = berendsen
> tc-grps  = rest_Protein SOL QMatoms
> tau_t= 0.1 0.1 0 ; QM atoms are uncoupled
> ref_t= 300 300 300
> Pcoupl   = Berendsen
> pcoupltype   = isotropic
> tau_p= 1.0
> compressibility  = 4.5e-5
> ref_p= 1.0
>  
> free_energy  = no
> init_lambda  = 0
> delta_lambda = 0
> QMMM = yes
> QMMM-grps= QMatoms
> QMmethod =
> QMbasis  =
> QMMMscheme   = normal
> QMcharge = -1
> CASelectrons =
> CASorbitals  =
> SH   =
>  
> gen_vel  = no
> gen_temp = 300
> gen_seed = 173529
>  
> constraints  = all-bonds
> constraint_algorithm = LINCS
> unconstrained_start  = yes
> shake_tol= 0.0001
> lincs_order  = 4
> lincs_warnangle  = 30
> morse= no
>   According to the instruction “In the ORCAINFO-file the method, basis set 
> and all other ORCA-specific keywords must be given. (This also means that 
> QMmethod and QMbasis from the mdp-file are ignored).”, the QMmethod and 
> QMbasis are blank, 
>But When grompp
> grompp_c -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o pyp_qm.tpr
> ……….
> Fatal error:
> Invalid QMMM input: 1 groups 0 basissets and 0 methods.
>  
> How to deal with it? Please help me!
> 
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[gmx-users] Re: 6. ORCA and dummy atom in the gromacs (xi zhao)

[Gerrit Groenhof]

 Did you run also your QM subsystem with the stand-alone version of Orca?

6. ORCA and dummy atom in the gromacs (xi zhao)



Gerrit
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[gmx-users] Re: orca and Segmentation fault (xi zhao)

[Gerrit Groenhof]

THe error message is clear: your spin multiplicity is 0, which is 
impossible.
Please make sure you understand the basics of electronic structure 
theory. To test this, you can run the QM system only in stand along QM 
package.


gerrit


2. Re: orca and Segmentation fault (xi zhao)
3. RE: Potential Energy Landscape (Natalie Stephenson)


-

./configure --without-qmmm-orca --without--qmmm-gaussian --enable-mpi
make
make install
I installed  gromacs with Parallel  mode,  is not threading. when I run  " mpirun 
-np 1 mdrun_dd -v -s pyp.tpr&" or mdrun_dd -nt 1Â -v -s pyp.tpr
it still"
Back Off! I just backed up md.log to ./#md.log.20#
Getting Loaded...
Reading file pyp.tpr, VERSION 4.5.1 (single precision)
Loaded with Money
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 22
QMlevel: B3LYP/3-21G
orca initialised...
Back Off! I just backed up traj.trr to ./#traj.trr.1#
Back Off! I just backed up traj.xtc to ./#traj.xtc.1#
Back Off! I just backed up ener.edr to ./#ener.edr.2#
starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water'
500 steps,      0.5 ps.
Calling 'orca pyp.inp>>  pyp.out'
Error : multiplicity (Mult:=2*S+1) is zero
---
Program mdrun_dd, VERSION 4.5.1
Source code file: qm_orca.c, line: 393
Fatal error:
Call to 'orca pyp.inp>>  pyp.out' failed
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
"The Carpenter Goes Bang Bang" (The Breeders)
Halting program mdrun_dd
gcq#129: "The Carpenter Goes Bang Bang" (The Breeders)
--
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--
--
mpirun has exited due to process rank 0 with PID 18080 on
node localhost.localdomai exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here)."


--- 11年11月14日，周一, Christoph Riplinger  
写�：


�件人: Christoph Riplinger
主题: Re: [gmx-users] orca and Segmentation fault
收件人: "Discussion list for GROMACS users"
日期: 2011年11月14日,周一,下�6:51





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[gmx-users] gromacs/mopac compilation: linking libmopac (Javier Cerezo)

[Gerrit Groenhof]

> 
>   3. Re: gromacs/mopac compilation: linking libmopac (Javier Cerezo)

Dear Javier,

Thanks for this update and your efforts. Can i put it on the website?

Could you check however the outcome (energy and forces) of an am1 or pm3 
computations with another program?

Best wishes,

Gerrit

> 
> Hi all
> 
> I post here the present status of my query in case my findings may be 
> helpful for someone else. In the case B (using gfortran to compile 
> libmopac) I have some success building g the gromacs binary for mdrun in 
> my x86_64 system.
> 
> **A
> Regarding the compilation with ifort, making test with simple C code I 
> relized that (at least in my case), it is needed to add some extra intel 
> libreries during compilation. Concretely I added the mkl libraries 
> (maybe libm was enough, but just in case) and the additional libraries 
> libifcore, libifcore_pic, libimf, libifport and libintlc (actually the 
> two that seem strongly required were libifcore and libintlc). The case 
> is that libintlc is only available in shared version, so I fist 
> recompiled my libmopac library with -fPIC flag:
> 
> ifort -O2 -fPIC -c *f; ar rcv libmopac.a *.o; ranlib  libifmopac.a
> 
> In my test C simple program, it was possible to link against the static 
> libifmopac.a while using other shared libraries (omitting the flag 
> -static), so I used --enable-shared. The configure script was 
> subsequently called as follows (with double precision as well):
> 
> ./configure --prefix 
> /home/cerezo/Programas/gromacs-4.5.5_with_ifort_mopac/ 
> --program-suffix=_d_ifmopac LDFLAGS="-L/home/cerezo/lib 
> -L/home/cerezo/lib/fftw/lib -L/usr/share/intel/mkl/lib/intel64 
> -L/usr/share/intel/lib/intel64" CPPFLAGS="-DUSE_MOPAC 
> -I/home/cerezo/lib/fftw/include" --with-qmmm-mopac 
> LIBS="-lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lifcore 
> -lifcore_pic -limf -lirc -lifport -lintlc -lifmopac" --disable-threads 
> --disable-float 
> LD_LIBRARY_PATH=/usr/share/intel/mkl/lib/intel64:/usr/share/intel/lib/intel64::LD_LIBRARY_PATH
> 
> Then
> 
> make mdrun -j 4
> 
> gave the following error:
> 
> cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 
> -funroll-all-loops -std=gnu99 -fexcess-precision=fast -o .libs/mdrun 
> gctio.o ionize.o do_gct.o repl_ex.o xutils.o runner.o md.o mdrun.o 
> genalg.o md_openmm.o  -L/home/cerezo/lib -L/home/cerezo/lib/fftw/lib 
> -L/usr/share/intel/mkl/lib/intel64 -L/usr/share/intel/lib/intel64 
> ./.libs/libgmxpreprocess_d.so 
> /home/cerezo/Programas/src/GROMACS_vX/gromacs-4.5.5/src/mdlib/.libs/libmd_d.so
>  
> ../mdlib/.libs/libmd_d.so /home/cerezo/lib/fftw/lib/libfftw3.so 
> /home/cerezo/Programas/src/GROMACS_vX/gromacs-4.5.5/src/gmxlib/.libs/libgmx_d.so
>  
> ../gmxlib/.libs/libgmx_d.so -lnsl -lm -lmkl_intel_ilp64 -lmkl_core 
> -lmkl_sequential -lifcore -lifcore_pic -limf -lirc -lifport -lintlc 
> -lifmopac  -Wl,--rpath 
> -Wl,/home/cerezo/Programas/gromacs-4.5.5_with_ifort_mopac/lib 
> -Wl,--rpath -Wl,/home/cerezo/lib/fftw/lib
> /home/cerezo/Programas/src/GROMACS_vX/gromacs-4.5.5/src/mdlib/.libs/libmd_d.so:
>  
> undefined reference to `__svml_asin2'
> /home/cerezo/Programas/src/GROMACS_vX/gromacs-4.5.5/src/mdlib/.libs/libmd_d.so:
>  
> undefined reference to `__svml_exp2_mask'
> collect2: ld returned 1 exit status
> make[1]: *** [mdrun] Error 1
> make[1]: se sale del directorio 
> «/home/cerezo/Programas/src/GROMACS_vX/gromacs-4.5.5/src/kernel»
> 
> 
> **B
> I succeeded to build gromacs/mopac with gfortran compiled libmopac. 
> Fisrt I compiled libmopac with:
> 
> gfortran -std=legacy -c *.f; ar rcv libmopac.a *.o; ranlib libmopac.a
> (I made the necessary changes to remove the warnings and errors, such as 
> changing the calls to SECOND(1) by SECOND() in polar.f and writmo.f)
> 
> In this case, gfortran procedures are simply linked with a single 
> library: libgfortran, with static version. Thus, I deactivated shared 
> option in the configure script. Then, the configure script for gromacs 
> looked like:
> 
>  ./configure --prefix 
> /home/cerezo/Programas/gromacs-4.5.5_with_gfor_mopac/ 
> --program-suffix=_d_mopac LDFLAGS="-L/home/cerezo/lib 
> -L/home/cerezo/lib/fftw/lib" CPPFLAGS="-DUSE_MOPAC 
> -I/home/cerezo/lib/fftw/include" --with-qmmm-mopac LIBS="-lmopac 
> -lgfortran" --disable-threads --disable-float -disable-shared
> 
> make mdrun -j 4
> 
> make install-mdrun
> 
> All worked correctly. However, I got a segmentation fault when running a 
> qm/mm calculation, the problem originated at libmopac subroutines. 
> Actually, the problem is in the subroutine FOCK2 (in fock2.f), at least 
> in my system compiling with gfortran: GNU Fortran (Ubuntu/Linaro 
> 4.5.2-8ubuntu4) 4.5.2. The work around comes as follows:
> 
> In fock2.f:
> Line 35:  IF(ICALCN.NE.NUMCAL) THEN
> [This if loop assures that variable initialization is only made the 
> fisrt time the main program calls the subroutine. However, in my 
> gfortran compiled binary, the variables were not saved from call

[gmx-users] 2. Re: GROMACS/ORCA QMMM (Jose Tusell)

[Gerrit Groenhof]

 On 11/22/2011 04:02 AM, gmx-users-requ...@gromacs.org wrote:

gmx-users@gromacs.org

To subscribe or unsubscribe via the World Wide Web, visit


 2. Re: GROMACS/ORCA QMMM (Jose Tusell)

Does anyone know what is going on with the coordinates of the QM
region?  Why are they not converted to the correct units?  Could
anyone point me to the error?

I have not experienced this myself. The only thing I can think of is that ORCA 
returns the atom coordinates in nm?
Does this happen also when you let Gromacs take care of the optimization?

Gerrit



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[gmx-users] Re: itp file for D2O (cuong nguyen)

[Gerrit Groenhof]

 Please check the paper by Grigera JCP 2001 114 8064 for the derivation 
for this model.


[ moleculetype ]
; molname   nrexcl
SOL 2

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
 1 OD  1SOL OW  1  -0.8715.99940
 2  D  1SOLHW1  1   0.4352.01600
 3  D  1SOLHW2  1   0.4352.01600

#ifdef FLEXIBLE
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.1 345000  0.1 345000
1   3   1   0.1 345000  0.1 345000

[ angles ]
; i j   k   funct   angle   force.c.
2   1   3   1   109.43  383 109.47  383
#else
[ settles ]
; OWfunct   doh dhh
1   1   0.1 0.16326

[ exclusions ]
1   2   3
2   1   3
3   1   2
#endif

in addition you need the LJ parameters for the OD and D (none actually)

   OD  8  0.000  0.000 A  0.0026160606 2.633235e-06
D  1  0.000  0.000 A  0 0



2. itp file for D2O (cuong nguyen)


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[gmx-users] Re: gmx-users Digest, Vol 92, Issue 56

[Gerrit Groenhof]

Does this also happen if you use pbc?
gerrit
On 10 Dec 2011, at 10:59, gmx-users-requ...@gromacs.org wrote:

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>   gmx-users@gromacs.org
> 
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> than "Re: Contents of gmx-users digest..."
> 
> 
> Today's Topics:
> 
>   1. qm/mm(orca/gromacs) (li yan)
> 
> 
> --
> 
> Message: 1
> Date: Sat, 10 Dec 2011 17:59:11 +0800
> From: li yan 
> Subject: [gmx-users] qm/mm(orca/gromacs)
> To: gmx-users@gromacs.org
> Message-ID:
>   
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear Gromacs developers:
> 
> I'm trying to run a QM-MM single point energy calculation on a
> structure (a small molecule with 50 water molecules with no pbc, no
> cutoff). I use orca for QM part amd gromacs for MM part. But when I
> run mdrun -nt 1 -s sp.tpr -c sp.gro -g sp.log, the ORCA run quickly
> and terminate naormally, but after that mdrun run stops with a
> segmentation fault. Here is the error information:
> 
> Back Off! I just backed up sp.log to ./#sp.log.1#
> 
> Reading file sp.tpr, VERSION 4.5.5 (single precision)
> 
> QM/MM calculation requested.
> 
> there we go!
> 
> Layer 0
> 
> nr of QM atoms 9
> 
> QMlevel: MP2/3-21G
> 
> /home/user/orca_x86_64_exe_r2360/home/user/programs/orca_x86_64_exe_r2360...
> 
> orca initialised...
> 
> Back Off! I just backed up traj.trr to ./#traj.trr.1#
> 
> Back Off! I just backed up ener.edr to ./#ener.edr.1#
> 
> starting mdrun 'Protein'
> 
> 0 steps,  0.0 ps.
> 
> Calling '/home/li/programs/orca_x86_64_exe_r2360/orca
> /home/li/Test/test_gmx/qmmm/test/sp.inp >>
> /home/li/Test/test_gmx/qmmm/test/sp.out'
> 
> Segmentation fault
> 
> Here is my sp.mdp
> 
> title= test
> 
> cpp  =/lib/cpp
> 
> integrator   = md
> 
> nsteps   = 0
> 
> dt   = 0.001
> 
> ;constraints = none
> 
> emtol= 10.0
> 
> emstep   = 0.01
> 
> nstcomm  = 1
> 
> ns-type  = simple
> 
> nstlist  = 0
> 
> rlist= 0
> 
> rcoulomb = 0
> 
> rvdw = 0
> 
> tcoupl   = no
> 
> pcoupl   = no
> 
> gen-vel  = no
> 
> nstxout  = 1
> 
> nstlog   = 1
> 
> nstenergy= 1
> 
> nstvout  = 1
> 
> nstfout  = 1
> 
> pbc  = no
> 
> comm_mode= angular
> 
> ; non-equilibrium md
> 
> freezegrps   = System
> 
> freezedim= y y y
> 
> xtc_grps = System
> 
> energygrps   = System
> 
> ;qmmm calculation
> 
> QMMM = yes
> 
> QMMM-grps= QMatoms
> 
> QMMMscheme   = normal
> 
> QMmethod = MP2
> 
> QMbasis  = 3-21g
> 
> QMcharge = 0
> 
> QMmult   = 1
> 
> The *.ORCAINFO is:
> 
> ! RKS b3lyp/g sv(p) tightscf
> 
> And I also tried QMMMsheme=ONIOM, but I get the segmentation fault
> too. Am I missing something in all of this?
> or the orca/gromcas can not be used  to non periodic system?
> Any help would be highly appreciated.
> 
> Thanks
> 
> Yan
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[gmx-users] Re: Alternative TRP residue

[Gerrit Groenhof]

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Message: 3
Date: Thu, 11 Jun 2009 17:09:41 +0200
From: abelius 
Subject: [gmx-users] Alternative TRP residue
To: gmx-users@gromacs.org
Message-ID: <4a311e35.7090...@gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Dear All,

I have AmberFF parameters for a TRP excited state and I was  
wondering if

it was possible to create an alternative TRP residue for gromacs?
Things I've done so far:
* Download and install amber99 for gromacs
* Add a new residue [ ETRP ] with adapted charges to the amber99.rtp  
file

* Add ETRP to aminoacids.dat

My question is where do I go from here, how can I add distances (bond
lengths) and angles?

Thank you very much,
Abel




--

Message: 4
Date: Thu, 11 Jun 2009 21:00:02 +0530
From: Manik Mayur 
Subject: [gmx-users] Re: Issues regarding exclusions and Charge group
distribution
To: Discussion list for GROMACS users 
Message-ID:
<7e56bc410906110830g2208ebcak4a42fa9fb3177...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi,

The last mail supposedly bounced from the server due to attachments.  
So

please excuse in case you find this as a repetition.

I am trying to simulate a system where I want to exclude all nb  
interactions

between frozen groups. So I followed the manual and defined them in
energygrp_excl. But upon doing that it throws the following warning.

WARNING 1 [file topol.top, line 1583]:
 Can not exclude the lattice Coulomb energy between energy groups

What is the reason of the warning and should I be worried about it  
or safely

ignore it.

Next, I am facing a strange problem with mdrun_mpi. If I run it on 4  
nodes
then it throws up the following error. Which I traced to md.log  
where I saw:


There are: 15923 Atoms
Charge group distribution at step 0: 0 3264 3185 0 (why these zeroes?)
Grid: 3 x 4 x 5 cells

However with 2 nodes it has and runs fine:

There are: 15923 Atoms
Charge group distribution at step 0: 3226 3223
Grid: 4 x 5 x 25 cells

The error-

Making 1D domain decomposition 1 x 1 x 4
starting mdrun 'TransverseElectrode'
10 steps,200.0 ps.
step 0

NOTE: Turning on dynamic load balancing

[md-comp1:32374] *** Process received signal ***
[md-comp1:32377] *** Process received signal ***
[md-comp1:32377] Signal: Segmentation fault (11)
[md-comp1:32377] Signal code: Address not mapped (1)
[md-comp1:32377] Failing at address: (nil)
[md-comp1:32374] Signal: Segmentation fault (11)
[md-comp1:32374] Signal code: Address not mapped (1)
[md-comp1:32374] Failing at address: (nil)
[md-comp1:32377] [ 0] [0xb7fd8440]
[md-comp1:32374] [ 0] [0xb7ef0440]
[md-comp1:32374] *** End of error message ***
[md-comp1:32377] *** End of error message ***

I would be extremely thankful, if somebody points me to the source  
of the

error and the workaround.

Thanks,

Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
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End of gmx-users Digest, Vol 62, Issue 59
*


--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://wwwuser.gwdg.de/~ggroenh/

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[gmx-users] Re: gmx-users Digest, Vol 62, Issue 68

[Gerrit Groenhof]

my gromacs version to 3.3.3 from 3.2.1. When I tried  
to run the pdb2gmx i got the follo: error. From the previous post I  
guess that i should edit this ffG43a1.hdb. but my input is a protein  
file so ..so is this necessary or any other way to rectify this  
problem???


---
Program pdb2gmx_mpi, VERSION 3.3.3
Source code file: h_db.c, line: 95

Fatal error:
Error in hdb file ffG43a1.hdb:
Wrong number of control atoms (2 iso 3) on line:
  1   1   N   -C  CA

Thanks in advance,
Aswathy
Dept. Biotechnology
Ext. 3108
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End of gmx-users Digest, Vol 62, Issue 68
*


--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://wwwuser.gwdg.de/~ggroenh/

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[gmx-users] Re: gmx-users Digest, Vol 64, Issue 17

[Gerrit Groenhof]

THere is documentation available in the manual and at
wwwuser.gwdg.de/~ggroenh/qmmm.html

If you need a SP computation, do a zero-step MD run: nsteps=0
Frequencies can only be computed numerically I think, but I never tried
this.

Best,

Gerrit

>7. QMMM settings (ilona.bal...@bioquant.uni-heidelberg.de)
>
>
>   
> Dear Gerrit,
>
> I am using Gromacs/Gaussian for qmmm-calculations. From the manual I  
> could only find the instructions for how to use qmmm the "normal way",  
> i.e. fill in the mdp file, but I learned from other Gromacs users that  
> adding additional keywords was possible. How? Where do I put them?
> Is there any documentation available on what the standard settings  
> are? i.e. every default qm step is a single-point calculation, right?  
> Is a zero point calculation included yet? If not, how can I change  
> from SP to frequency calculation?
>
> Best wishes and thanks in advance, Ilona
>
>
> --
>
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> End of gmx-users Digest, Vol 64, Issue 17
> *
>   

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[gmx-users] Re: 3 covalent bonds protein- heme (malve...@iq.usp.br)

[Gerrit Groenhof]

You can use the specbond file:

and add entries like:

HID NE2 1 HEME FE 1 0.25 HID HEME

and run pdb2gmx with the -merge option.

Best

Gerrit



  4. 3 covalent bonds protein- heme (malve...@iq.usp.br)
  --

Message: 4
Date: Wed, 16 Sep 2009 18:40:16 -0300
From: malve...@iq.usp.br
Subject: [gmx-users] 3 covalent bonds protein- heme
To: gmx-users@gromacs.org
Message-ID: <20090916184016.7kfq1r9svcow4...@webmail.iq.usp.br>
Content-Type: text/plain;   charset=ISO-8859-1; DelSp="Yes";
format="flowed"

Dear Friends,
I have to make three covalent bonds between the protein and the heme  
group.

I have parameters for heme and the residues.
Do I have to make as if everything belongs to the same molecule?  (as
it realy is)
Has anyone done something like this?
Thanks
Alberto



--

Message: 5
Date: Thu, 17 Sep 2009 09:08:20 +0800
From: Yang Ye 
Subject: Re: [gmx-users] compiling problem
To: Discussion list for GROMACS users 
Message-ID:
<1b3c3eeb0909161808s2e01a4c9p3ce0a43646edc...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Just a work-around, force mpicc to point to cc.
alias mpicc=cc

Yang Ye

On Wed, Sep 16, 2009 at 5:35 PM, Mu Yuguang (Dr)   
wrote:



No, even I do not use mpi , the error is still there.



Regards

Yuguang


 --

*From:* gmx-users-boun...@gromacs.org [mailto:
gmx-users-boun...@gromacs.org] *On Behalf Of *Yang Ye
*Sent:* Wednesday, September 16, 2009 2:34 PM
*To:* Discussion list for GROMACS users
*Subject:* Re: [gmx-users] compiling problem



Is LAM-MPI's binary in PATH? if you run mpicc from console, will it  
also

show "No such file or directory"? Check LAM-MPI installation.

Regards,
Yang Ye

On Wed, Sep 16, 2009 at 12:39 PM, Mu Yuguang (Dr)   
wrote:


Hi,
I use
git clone git://git.gromacs.org/gromacs.git

to get the lastest version
and
./bootstrap

To generate the configure file
Then use ./configure successfully

Howeve, after make
The error appears as foloowing:


mpicc -DHAVE_CONFIG_H -I. -I. -I../../../../src -I/usr/X11R6/include
-I/usr/include/libxml2 -I../../../../include
-DGMXLIBDIR=\"/home/ygmu/software/gmx_cvs/gromacs/share/top\"
-I/home/ygmu/software/fftw-3.2/float/include -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops - 
std=gnu99
-MT nb_kernel400_x86_64_sse.lo -MD -MP -MF .deps/ 
nb_kernel400_x86_64_sse.Tpo

-c nb_kernel400_x86_64_sse.c -o nb_kernel400_x86_64_sse.o
nb_kernel400_x86_64_sse.c: In function `nb_kernel400_x86_64_sse':
nb_kernel400_x86_64_sse.c:93: warning: implicit declaration of  
function

`_mm_castsi128_ps'
nb_kernel400_x86_64_sse.c:93: error: invalid initializer
nb_kernel400_x86_64_sse.c:94: error: invalid initializer
nb_kernel400_x86_64_sse.c:95: error: invalid initializer
mpicc: No such file or directory
make[5]: *** [nb_kernel400_x86_64_sse.lo] Error 1

Regards

Yuguang
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Yang Ye

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End of gmx-users Digest, Vol 65, Issue 96
*


--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://wwwuser.gwdg.de/~ggroenh/

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[gmx-users] Re: gmx-users Digest, Vol 65, Issue 83 6. EVB and mapping potentials (rsf)

[Gerrit Groenhof]

Hi,

I think that you could use the free energy parts of gromacs for your
purposes.

V1 and V2 can be coupled via a parameter lambda, such that (assuming
you're not changing masses/atoms)
H(p,r,lambda) = (1-lambda)* V(A-B + C) + lambda*V(A + B-C).

IN the manual it is described how to inform gromacs what V(A-B + C)  and
V(A + B-C) are.

For new bonds, angles etc, define them all, but let the forceconstants
and equilibrium constants be 0 in one state, like:

A-B 1 r_e k 0 0
B-C 1 0 0 r_e k


For driving it, you can perform the MD at discrete lambda values along
the 0,1 interval.

Hope this helps.

Best,

Gerrit

> Hi
>
> Thanks for you answer, what I want to do is to study a reaction with MD
>
> A-B +C -> A+B-C
>
> , for that I am representing it by a two state system in an EVB
> representation, where I have my transferring group, B, attached to A in
> the first state(V1) and to C in the second(V2). I am describing the
> off-diagonal elements as a constant parameter fitted form experimental
> data to reproduce the experimental free energy profile.
>
> To sample the space I would like to drive the reaction using a mapping
> potential of the form
>
> Vmap= V1 + lamda*(V2-V1), with lambda ranging from [0.0,1.0].
>
> Therefore I would have to get gromacs to run on the potential surface
> generated by the mapping potential, which is a mixture of my two diagonal
> states. I have been trying to see if gromacs can deal with this situation
> with the present implementation, but I can't seem to find what I need. I
> can also program it in myself, but I would like to know if someone has an
> idea of how to do it properly within the existing framework of gromacs, or
> if someone is aware of some way of getting the current version of gromacs
> to do what I need.
>
> The difference between both states would be some topology parameters
> (charges, bonds, angles, dihedrals) as well as connectivities that
> describe the chemically active part of the system.
>
> Thanks so much for your comments.
>
> Romelia
>   
>>>6. EVB and mapping potentials (rsf)
>>>
>>>   
>> Hi,
>>
>> I do not understand your question, but what you try to do seems
>> interesting.
>>
>> This is how far I got:
>>
>> If you have only two states to interconnect, the diagonal elements would
>> be the energy H(lamda=0) and H(lamda=1). The off diagonals then have to be
>> parametrized as a function of lambda? Would diagonalization then give you
>> the forces on lambda?
>>
>> We have a version of gromacs which supports lambda dynamics, but I am not
>> sure if that's what you need?
>>
>> Best,
>>
>> Gerrit
>>
>>
>> 
>>> Hi
>>>
>>> I want to describe a reaction for what I have a system described by two
>>> different connectivities and need to run an MD calculation on a mapping
>>> potential of the type V1- C (V2-V1), where V1 and V2 are my diagonal
>>> elements of the evb matrix and C is a parameter. Does gromacs have
>>> support
>>> for running something like this?. Which would be the best way to run
>>> this
>>> calculation with the standard code, or should I modify it in order to do
>>> that. The states have some atoms with different connectivity between
>>> them,
>>> different forcefield parameters and different charges, the atom types
>>> are
>>> the same for both.
>>>
>>>
>>> Thanks for your comments.
>>>
>>>
>>> Romelia.
>>>
>>> --
>>> 
>>> Romelia Salomon
>>> Miller Group
>>> 132 Noyes
>>> Chemistry Department
>>> Caltech
>>>
>>>
>>>
>>>
>>> --
>>>
>>> ___
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>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>> posting!
>>>
>>> End of gmx-users Digest, Vol 65, Issue 81
>>> *
>>>
>>>   
>> ___
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>>
>> 
>
>
>   

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[gmx-users] QM/MM topology fiels problem

[Gerrit Groenhof]

 Please read the error message: it says that you need no parameters for 
your conn bonds.


Gerrit





Message: 2
Date: Tue, 21 Sep 2010 14:58:40 +0530 (IST)
From: vidhya sankar
Subject: [gmx-users] QM/MM topology fiels problem
To: gmx-users@gromacs.org
Message-ID:<277598.19746...@web95503.mail.in.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Dear gromacs users , thank you for your reply
  when i run the
  ./grompp it shows the error as follows
./grompp_d -f em.mdp -c spep_b4em.gro -p spep.top -o spep_em.tpr

ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6bon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 222 of the 1653 non-bonded parameter combinations
---
Program grompp_d, VERSION 4.0.7
Source code file: toppush.c, line: 1379

Fatal error:
Incorrect number of parameters - found 2, expected 0 or 0 for Connect Bonds
what could i do to avod error? i am expecting your valuable reply


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Message: 3
Date: Tue, 21 Sep 2010 11:57:22 +0200 (MEST)
From: Fabio Affinito
Subject: Re: [gmx-users] error on compilation on BlueGene/P
To: Discussion list for GROMACS users
Message-ID:<4c988143.9020...@cineca.it>
Content-Type: text/plain; charset=ISO-8859-1

Like for the frontend, the --enable-fortran is the problem.
Maybe it could be useful to update the instruction page :)

Fabio


On 09/21/2010 10:54 AM, Mark Abraham wrote:


- Original Message -
From: Fabio Affinito
Date: Tuesday, September 21, 2010 18:51
Subject: Re: [gmx-users] error on compilation on BlueGene/P
To: Discussion list for GROMACS users


Thank you, Mark and Berk!
your suggestion was helpful and I successfully compiled on the
frontend.Now I have a problem when I compile on the compute nodes.
Configure was fine with these parameters:

../configure --prefix=/bgp/userinternal/cin0644a/gromacs \
   --host=ppc --build=ppc64 --enable-ppc-sqrt=1 \
   --disable-ppc-altivec \
   --enable-bluegene --enable-fortran --enable-mpi \
   --with-fft=fftw3 \
   --program-suffix=_mpi_bg \
   --without-x \
  CC=mpixlc_r \
  CFLAGS="-O3 -qarch=450d -qtune=450" \
  MPICC=mpixlc_r CXX=mpixlC_r \
  CXXFLAGS="-O3 -qarch=450d -qtune=450" \
  CPPFLAGS="-I/bgp/userinternal/cin0644a/fftwlibs/include" \
  F77=mpixlf77_r FFLAGS="-O3 -qarch=auto -qtune=auto" \
  LDFLAGS="-L/bgp/userinternal/cin0644a/fftwlibs/lib" \
  LIBS="-lmass"

But when I compile using "make mdrun" the compilation stops in
this way.

creating libgmxpreprocess_mpi.la
(cd .libs&&  rm -f libgmxpreprocess_mpi.la&&  ln -s
../libgmxpreprocess_mpi.la libgmxpreprocess_mpi.la)
make[1]: *** No rule to make target `../mdlib/libmd_mpi.la',
needed by
`mdrun'.  Stop.
make[1]: Leaving directory
`/bgp/userinternal/cin0644a/gmx/bgp/src/kernel'
Any suggestion? Thanks!


Normally that would be symptomatic of an earlier error in make (or maybe
configure). Please check carefully.

Mark





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[gmx-users] Re: gmx-users Digest, Vol 77, Issue 142

[Gerrit Groenhof]

Why do you try to do MP2. Mopac will only allow semi-empirical methods. Though 
that does not seem to be the source of the error.

Gerrit

further when i run Mdrun after energy minimisatins by following command
./mdrun_d -s spep_em.tpr -o spep_em.trr -c spep_b4pr.gro -g em.log
I got errror as follows i am using Mopac/gromacs intrface
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 14
QMlevel: MP2/STO-3G

number of CPUs for gaussian = 1
memory for gaussian = 5000
accuracy in l510 = 8
NOT using cp-mcscf in l1003
Level of SA at start = 0
Segmentation fault (core dumped)

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[gmx-users] Re: gmx-users Digest, Vol 78, Issue 123

[Gerrit Groenhof]

3. Simulation parameter problem about protein unfolding (Chen)



Hi,

You write it yourself: In paper you mention, they have used a 0.8 nm 
cutoff range for both electrostatics and cutoff. You are doing something 
different by using PME for the electrostatics. Also you are using a much 
longer cutoff for the VDW interactions.


If you want to reproduce their results, you need to stick to to the 
parameters mentioned in that paper and use cut-offs as well.


BTW I do not believe this to be a good idea though.

Gerrit



Hi All,

I met a problem when I try to unfold a protein using Gromacs, It seemed the 
protein cannot be totally unfolded!

The simulated system has one Engrailed Homeodomain (En) protein (a three helix 
bundle protein with 54 residues, 629 atoms), total 4848 spce waters, and 7 Cl- 
used to neutralize the system in a 5.752(nm)3  water BOX. I use the NTP 
ensemble with T=498K and P=26atm. The system has 1nm thick water in each side 
of the En protein, and the density of the system has been adjusted to0.829 
g/cm3.

The simulation lasted 24ns. The helixes disappeared at about 4ns. And after 
that some beta sheet formed in the N terminal of the protein. However, the 
protein kept in a compact state during the 24ns simulation. The radius of 
gyration of the protein fluctuated around 1.1nm during the simulation.

I've also noticed similar simulation done by others. For example, David Becka and Valerie 
Daggett reviewed their En protein unfolding in paper "Methods for molecular dynamics 
simulations of protein folding/unfolding in solution. Methods 34 (2004) 112¨C120". 
The simulations were performed with ENCAD and ilmm, and used an 0.8nm cutoff range. And 
the ensemble they used is NVE as I know. A stretched unfolding state occurred at about 
5ns in their 60ns simulation in 498K, with little helix structure.

I was wondering whether the difference is caused by using different MD software 
and force field, or by some wrong parameters in my .mdp file. I've also 
conducted another 18ns simulation, and the result is almost the same. I list he 
mdp file below. Any comment is appreciated!

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Subject: Re: [gmx-users] GFP chromophore topology help

[Gerrit Groenhof]

Can you perform a simulation of the chromophore alone? 
Does that stay stable?

Gerrit

> Date: Sat, 13 Nov 2010 12:32:04 -0800
> From: Ramachandran G 
> Subject: Re: [gmx-users] GFP chromophore topology help
> To: jalem...@vt.edu, Discussion list for GROMACS users
>   
> Message-ID:
>   
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Thank you, Justin..
> 
> I added the all the needed connectivity for GFP chromophore in the
> aminoacid.rtp(mentioned -C and +N to indicate the preceding and
> following residue) and also defined the residue as "Protein" in
> residuetypes.dat. For the non existing bond types, bond angles, proper
> and improper dihedrals, i added newly in the file ffbonded.itp. Also
> hydrogen atom connectivity are defined in the .hdb file.
> 
> The structure looks perfect after pdb2gmx but when i do minimization,
> the atoms(N+ and C-) chromphore along with neighbouring residue
> terminals are flying apart. So i don't know where i am making
> mistakes.
> 
> Should i need to give information in the Termini database flie *.tdb ? or
> Is this due to wrong force constant values?  or
> Is my force field parameter has mistakes?
> 
> Thank your for you help.
> Rama
> 
> On Fri, Nov 12, 2010 at 6:20 PM, Justin A. Lemkul  wrote:
>> 
>> 
>> Ramachandran G wrote:
>>> 
>>> Thank you for the help.
>>>  I have successfully constructed the chromphore molecule but
>>> still have problem in connecting it to the neigbhouring residues. I
>>> don't know how the connection sequence needs to be given in gromacs.
>>> Please help
>>> 
>> 
>> You stand a much better chance of getting useful help if you at least
>> describe what you attempted and why it didn't work.  For the GFP
>> chromophore, which incorporates into the backbone, you need to add
>> connectivity in the .rtp file like any other amino acid residue (-C and +N),
>> and define the residue as "Protein" in residuetypes.dat (if using version
>> 4.5.x).  Without knowing what you've done, though, I'm only guessing.
>> 
>> -Justin
>> 
>>> with regards,
>>> Rama
>>> 
>>> On Tue, Nov 9, 2010 at 3:22 PM, Justin A. Lemkul  wrote:
>>>> 
>>>> Ramachandran G wrote:
>>>>> 
>>>>> Dear gromacs users:
>>>>> 
>>>>>  I have constructed the Amber03 force fields parameters
>>>>> (bonds,angles, proper and imporer dihedral.) for the chromophore
>>>>> (p-hydroxybenzylidene-imidazolinone) inside GFP system and got the
>>>>> topology. But after energy minimization of the system, the
>>>>> conformation of the chromophore totally changed and the benzene and
>>>>> imidazole ring got puckered although i did not got any error message.
>>>>> 
>>>> No Gromacs tool will check your work for you.  It will do what you tell
>>>> it.
>>>> Likely you omitted some necessary bonded parameters (bonds, angles,
>>>> impropers, etc).  Either that, or the parameters you supplied produce the
>>>> incorrect behavior.
>>>> 
>>>> -Justin
>>>> 
>>>>> Could anyone help me? Thank you.
>>>>> 
>>>>> 
>>>>> with regards,
>>>>> Rama
>>>> 
>>>> --
>>>> 
>>>> 
>>>> Justin A. Lemkul
>>>> Ph.D. Candidate
>>>> ICTAS Doctoral Scholar
>>>> MILES-IGERT Trainee
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>> 
>>>> 
>>>> --
>>>> gmx-users mailing listgmx-users@gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>> interface
>>>> or send it to gmx-users-requ...@gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>> 
>>> 
>>> 
>>> 
>> 
>> --
>> 
>> 
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Docto

[gmx-users] Re: MOPAC gromacs mdreun error (vidhya sankar)

[Gerrit Groenhof]

> 
>   2. MOPAC gromacs mdreun error (vidhya sankar)

It seems that you are trying to run with multiple threads. Use mdrun -nt 1 to 
use only a single thread.

Gerrit


> Dear gmx users
> 
> i have successfuly installed Mopac gromacs/interface. but when i run 
> the QM/MM in mdrun_d 
>  i have got hte following error 
> QM/MM calculation requested.
> QM/MM calculation requested.
> there we go!
> there we go!
> Segmentation fault (core dumped)
> i am using 6 atoms for my Qm region i am using fedora core13 OS and pentium 
> intel i5
> what could i do to remove this error
> ?
> i am expecting your reply soon  thanks in advance
> 
> 
> 
--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://wwwuser.gwdg.de/~ggroenh/

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Subject: [gmx-users] : MOPAC gromacs mdreun error (vidhya sankar)

[Gerrit Groenhof]

 Please check if your stand-alone mopac binary works properly. Also 
check if the mdrun binary is linked against the libmopac.a


Gerrit

Message: 2
Date: Mon, 6 Dec 2010 11:55:58 +0530 (IST)
From: vidhya sankar
Subject: [gmx-users] : MOPAC gromacs mdreun error (vidhya sankar)
To: gmx-users@gromacs.org
Message-ID:<157886.66733...@web95506.mail.in.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear Gerrit  sir,
Thank you for your previous reply i tried as u said with  -nt 1 
option in mdrun but still i have got hte following error when i run mdrun_d
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 2
QMlevel: PM3/STO-3G
Program mdrun_d, VERSION 4.5.3
Source code file: qmmm.c, line: 697
Fatal error:
Semi-empirical QM only supported with Mopac.
  but i configured gromacs properly with mopac. how to solve the problem
  is ther is any link that i have not made available ? i am expecting your 
worthfull reply thanks isn advance




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[gmx-users] Re: gmx-users Digest, Vol 80, Issue 41

[Gerrit Groenhof]

Without-qmmm-mopac will not lead to compilation of the mopac interface source 
code. 

What is the compilation error?

Gerrit



> 
>   1. MOPAC gromacs mdreun error (vidhya sankar) (vidhya sankar)
>
> 
> Message: 1
> Date: Mon, 6 Dec 2010 18:34:00 +0530 (IST)
> From: vidhya sankar 
> Subject: [gmx-users] MOPAC gromacs mdreun error (vidhya sankar)
> To: gmx-users@gromacs.org
> Message-ID: <665887.73042...@web95501.mail.in.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear Gerrit sir,
>   Thank you for your atonce reply 
> my mopac stand alone binary works well  i have tested using ./run_mopac7 
> tests/force
> but mdrun is not properly linked aganist libmopac.a 
>  i am using the following command to  configure 
> ./configure --disable-float --without-qmmm-mopac CPPFLAGS=-DUSE_MOPAC 
> LIBS=-lmopac LDFLAGS=-L/usr/local/lib
> if i use --with-qmmm-mopac i end in  make error (compilation  error) 
>  also how to check how to check the link of mdrun aganist libmopac.a  is 
> there is any command for this?
> i am expecting your precious reply thanks in advance
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> --- On Mon, 6/12/10, Gerrit Groenhof  wrote:
> 
> From: Gerrit Groenhof 
> Subject: Subject: [gmx-users] : MOPAC gromacs mdreun error (vidhya sankar)
> To: gmx-users@gromacs.org
> Date: Monday, 6 December, 2010, 12:57 PM
> 
> Please check if your stand-alone mopac binary works properly. Also check if 
> the mdrun binary is linked against the libmopac.a
> 
> Gerrit
>> Message: 2
>> Date: Mon, 6 Dec 2010 11:55:58 +0530 (IST)
>> From: vidhya sankar
>> Subject: [gmx-users] : MOPAC gromacs mdreun error (vidhya sankar)
>> To: gmx-users@gromacs.org
>> Message-ID:<157886.66733...@web95506.mail.in.yahoo.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>> 
>> Dear Gerrit  sir,
>>  Thank you for your previous reply i tried as u said with  
>> -nt 1 option in mdrun but still i have got hte following error when i run 
>> mdrun_d
>> QM/MM calculation requested.
>> there we go!
>> Layer 0
>> nr of QM atoms 2
>> QMlevel: PM3/STO-3G
>> Program mdrun_d, VERSION 4.5.3
>> Source code file: qmmm.c, line: 697
>> Fatal error:
>> Semi-empirical QM only supported with Mopac.
>>but i configured gromacs properly with mopac. how to solve the problem
>>is ther is any link that i have not made available ? i am expecting your 
>> worthfull reply thanks isn advance
>> 
>> 
> 
> -- gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface 
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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> --
> 
> Message: 2
> Date: Mon, 06 Dec 2010 18:40:36 +0100
> From: Sebastian Fritsch 
> Subject: Re: [gmx-users] Constraining two virtual sites
> To: gmx-users@gromacs.org
> Message-ID: <4cfd2014.1080...@mpip-mainz.mpg.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Hi again,
> 
> 
> unfortunately I would need the constraint for a large number of molecules, 
> say ~1000 i.e. 2000 vsites representing a few atoms each.
> The constraint length should however be the same for each molecule. 
> 
> Assigning groups for each constraint group would not be possible due to the 
> group limit I guess.
> The do_constraint function in pull.c does not look too complicated, do you 
> think it would be reasonable to adapt it a bit and call it
> from some function like calc_bonds which comes after vsite construct and 
> before vsite spread? The constraint forces in my case should be
> be completely determined by the vsites, or am I wrong? Is there an easier 
> solution?
> 
> 
> Thank you,
> Sebastian
> 
>> Hi,
>> 
>> Unfortunately constraints can not be applied to virtual sites and grompp 
>> apparently
>> does not not check for this. I will add a check.
>> Constraints between virtual sites can lead to very complex constraint 
>> equations
>> between the masses involved. Thus the general case if difficult to implement.
>> Your cases seems quite simple

[gmx-users] Re:6. QMMM, Segmentation fault (Olga Ivchenko)

[Gerrit Groenhof]

Dera gromacs users,

I am trying to do QMMM in the latest gromacs version :gromacs-4.5-beta2.
When I run DFT I got an error:

number of CPUs for gaussian = 1
memory for gaussian = 5000
accuracy in l510 = 8
NOT using cp-mcscf in l1003
Level of SA at start = 0
Segmentation fault

Are you trying to use more than one thread?

Gerrit

Please could you advice me on this?


6. QMMM, Segmentation fault (Olga Ivchenko)




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[gmx-users] Re: Re:6. QMMM, Segmentation fault (Olga Ivchenko) (Olga Ivchenko)

[Gerrit Groenhof]

 Try to run with mdrun -nt 1




1. Re: Re:6. QMMM, Segmentation fault (Olga Ivchenko) (Olga Ivchenko)
2. group temperatures and kinetic energies (Dmitri Dubov)
3. Re: group temperatures and kinetic energies (Dmitri Dubov)


--

Message: 1
Date: Wed, 8 Dec 2010 10:19:00 +0100
From: Olga Ivchenko
Subject: Re: [gmx-users] Re:6. QMMM, Segmentation fault (Olga
Ivchenko)
To: Discussion list for GROMACS users
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

Actually I am not sure that I can understand what is thread. But I can paste
QMMM file here:



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[gmx-users] 4. Requesting advice on pressure scaling in a protein-in-membrane system. (Daniel Adriano Silva M)

[Gerrit Groenhof]

Can you simulate the membrane and protein seperately, thus the two system you 
are trying to merge?

Gerrit

> 
>  4. Requesting advice on pressure scaling in a
> protein-in-membrane system. (Daniel Adriano Silva M)
> 


> 
> Dear gmx users and developers,
> 
> I am facing a problem that is new for me and I will appreciate advice from
> your expertise. I am working with a big protein complex (around 100K atoms,
> several subunits) and I used g_membed to embed it in a (aprox 24 14 nm)
> pre-equilibrated POPC membrane, however after embedding and a 1ns of NVT
> equilibration I tried to proced to the NPT equilibration, but I found my
> system exploding (things moving to fast), so I tried several methods that
> came to my mind (like decrease the P-coupling constant, decrease the
> timestep and some others). After few tries I went back to the
> NVT  equilibration and took a look to the pressure, for my surprise I found
> it to be around 1e30! So I ended with a very compressed system on X-Y, I
> guess given the embedding of the protein in the membrane. Here are the
> questions:
> 
> 1) Are there any reasonable simple method to reduce the pressure on the
> protein/lipid system?
> 2) May I expect a very long time to reach the adequate pressure and
> equilibrium given a possible change on the phase of the lipids by the high
> pressure?
> 3) Any other useful direction?
> 
> Extra information: On this step I had frozen the Protein and excluded the
> Protein-Protein energy.
> 
> Thanks,
> Daniel Silva
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> 
> --
> 
> Message: 5
> Date: Fri, 07 Jan 2011 10:07:27 -0500
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] Requesting advice on pressure scaling in a
>   protein-in-membrane system.
> To: Discussion list for GROMACS users 
> Message-ID: <4d272c2f.2070...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> 
> Daniel Adriano Silva M wrote:
>> Dear gmx users and developers,
>> 
>> I am facing a problem that is new for me and I will appreciate advice 
>> from your expertise. I am working with a big protein complex (around 
>> 100K atoms, several subunits) and I used g_membed to embed it in a 
>> (aprox 24 14 nm) pre-equilibrated POPC membrane, however after embedding 
>> and a 1ns of NVT equilibration I tried to proced to the NPT 
>> equilibration, but I found my system exploding (things moving to fast), 
>> so I tried several methods that came to my mind (like decrease the 
>> P-coupling constant, decrease the timestep and some others). After few 
>> tries I went back to the NVT  equilibration and took a look to the 
>> pressure, for my surprise I found it to be around 1e30! So I ended with 
>> a very compressed system on X-Y, I guess given the embedding of the 
>> protein in the membrane. Here are the questions:
>> 
>> 1) Are there any reasonable simple method to reduce the pressure on the 
>> protein/lipid system?
>> 2) May I expect a very long time to reach the adequate pressure and 
>> equilibrium given a possible change on the phase of the lipids by the 
>> high pressure?
>> 3) Any other useful direction?
>> 
>> Extra information: On this step I had frozen the Protein and excluded 
>> the Protein-Protein energy.
>> 
> 
> During NVT?  Turn off this freezing before proceeding, doing additional NVT 
> if 
> necessary.  Frozen groups can do weird things, and I would suspect that your 
> system simply isn't stable in the presence of these frozen groups.
> 
> I have a procedure (and troubleshooting tips) for equilibrating membrane 
> protein 
> systems in my tutorial:
> 
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
> 
> You may find it useful.  Membrane systems do take a while to converge, but 
> that's not your issue here.  You have some fundamental instability to deal 
> with 
> first.
> 
> -Justin
> 
>> Thanks,
>> Daniel Silva
>> 
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> 

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[gmx-users] Re: QMMM with ORCA

[Gerrit Groenhof]

Dear Xiaohu,

Thanks for bringing this up. The comment has been there for ever. Since I could 
not think of an application where one would not be using pbc at the time. 
However, your clusters prove me wrong.

In any case, as a work-around, you may want to use a bigger box, with long 
enough cut-offs, no PME.

Hope this gets you started,

Gerrit

On 27 Jan 2011, at 21:02, Xiaohu Li wrote:

> Dear GMX code writters,
>  Could anyone tell me why this comments in the code mdlib/qmmm.c 
> appear?(version 4.5.3)
> at line ~ 714, in the beginning of subroutine update_QMMMrec
> ==
> /* updates the coordinates of both QM atoms and MM atoms and stores
>* them in the QMMMrec.  
>*
>* NOTE: is NOT yet working if there are no PBC. Also in ns.c, simple
>* ns needs to be fixed!  
> */
> ==
> First of all, I have a non-PBC job with electronic embedding and it 
> fails right in this routine. So I guess this is the reason, for non-PBC, it 
> crashes. But for oniom, it went through. Is there any simple fix to have the 
> non-PBC qmmm work? I'm also interested in doing non-PBC calculation(large 
> cluster).
> 
> 
> Xiaohu
> 
> On Thu, Jan 27, 2011 at 9:11 AM, Christoph Riplinger  
> wrote:
> Hi Xiaohu,
> 
> We are using gromacs/ORCA quite a lot. It works like any of the other 
> interfaced programs and whether you should use it depends on your needs to 
> the QM part of the QM/MM calculation.
> 
> I am using gromacs 4.0.7, but I downloaded the 4.5.3 version to test it.
> 
> I could not reproduce your problem with ONIOM. For the electrostatic 
> embedding bug, I agree. This didn't work in my test calculation, but my gdb 
> told me that the abort occured before the qm_orca.c was even called. I 
> suspect the bug is in the general qmmm.c code. I do not have access to the 
> other QM-programs and cannot test this, so if you have, could you please run 
> the same job with a different QM-program. 
> 
> Hope that helps
> 
> Christoph
> 
> 
> 
> 
> On 01/26/2011 06:48 AM, Xiaohu Li wrote:
>> 
>> Hi, All,
>>  I'm trying to see if anybody has experience of using the interface of 
>> gromacs and ORCA(since it's free). I know that the following link gave 
>> information on how
>> http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code
>>  But.But, the gromacs in the above link is quite old(3.2). I 
>> download the latest 4.5.3 and followed the instructions in the above link 
>> and I was trying to optimize an simple cluster(no pbc) where part of it are 
>> treated using QM. here is the example mdp file
>> =
>> title   =  cpeptide
>> integrator  =  steep   ;integrator includes energy minimization 
>> algorithms
>> dt  =  0.002; ps !
>> nsteps  =   1
>> nstlist =  1
>> ns_type =  simple
>> rlist   =  3.0
>> rcoulomb=  3.0
>> coulombtype = cut-off
>> vdwtype = cut-off
>> rvdw= 3.0
>> pbc =  no
>> periodic_molecules  =  no
>> constraints = none
>> energygrps  = qm_part mm_part
>> ; QM/MM calculation stuff
>> QMMM = yes
>> QMMM-grps = qm_part
>> QMmethod = rhf
>> QMbasis = 3-21G
>> QMMMscheme = oniom
>> QMcharge = 0
>> QMmult = 1
>> ;
>> ;   Energy minimizing stuff
>> ;
>> emtol   =  60   ; minimization thresold (kj/mol.nm-1)1 
>> hartree/bohr= 49614.75241 kj/mol.nm-1  1 kj/mol.nm-1=2.01553e-5 hartree/bohr
>> emstep  =  0.01  ; minimization step in nm
>> =
>> I set up the BASENAME and ORCA_PATH as told in the instruction.
>> first of all, the normal electronic embedding just simply gave segmentation 
>> fault error right after the it prints information on number of steps of 
>> optimization.
>> 
>> So I switch to ONIOM, this time, at least, orca is called and energy and 
>> gradient are both generated. However, when it comes to read the energy and 
>> gradient, it always crashes when tried to read gradient, this is at line 346 
>> source code src/mdlib/qm_orca.c
>> 
>> sscanf(buf,"%lf\n", &QMgrad[k][XX]);
>> 
>> a segmentation fault error is printed. If I replace the &QMgrad[k][XX] by an 
>> temporary variable temp 
>>  sscanf(buf,"%lf\n", &temp);
>> temp gets the correct value and if I use,
>> QMgrad[k][XX]=temp 
>> and tries to print QMgrad[k][XX], a bus error will be printed.
>> I did some research online, seems that usually this implies an memory bug in 
>> the code which is the most difficult bug one can ever encounter.
>> So has anyone successfully used gromacs and orca to do QM

[gmx-users] Re: 1. Normal mode analysis of pure water (simon sangma)

[Gerrit Groenhof]

If you are interested in the IR spectrum of water, all you need to do  
is a simulation of a flexible water model (not flexspc btw), save  
every fs, compute the dipole moment, compute the powerspectrum of that  
dipole moment and check for the peaks.


Gerrit



(tip3p_flex for instance, by skinner)




  1. Normal mode analysis of pure water (simon sangma)
  2. Normal mode analysis of pure water (simon sangma)
  3. Re: Normal mode analysis of pure water (Justin A. Lemkul)
  4. Re: AMBER force fields in gromacs program (Justin A. Lemkul)
  5. Re: Error during NVT equillibration with nvt.log file (ram bio)
  6. Re: Error during NVT equillibration with nvt.log file
 (Justin A. Lemkul)


--

Message: 1
Date: Tue, 20 Oct 2009 19:46:56 +0530
From: simon sangma 
Subject: [gmx-users] Normal mode analysis of pure water
To: gmx-users@gromacs.org
Message-ID:
<93e0339c0910200716x52cc241bq2861cc0638d7...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi Berk,
I want to determine the vibrational frequencies of water  
(close
to the experimentally observed values for the three modes). And then  
extend

the analogy for more complex systems.

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[gmx-users] Re: access code for qmmm (Farzad Molani)

[Gerrit Groenhof]

Yesterday Ilona has already given the information for you to formulate  
a new question. So be more specific about what problem you have now.


Best,

Gerrit




Today's Topics:

  6. Re: access code for qmmm (Farzad Molani)
  7. RE: access code for qmmm (Kukol, Andreas)
  8. Urea Topology (karan syal)

Message: 6
Date: Tue, 17 Nov 2009 00:56:31 -0800 (PST)
From: Farzad Molani 
Subject: Re: [gmx-users] access code for qmmm
To: Discussion list for GROMACS users 
Message-ID: <843559.85861...@web55703.mail.re3.yahoo.com>
Content-Type: text/plain; charset="us-ascii"

Hello,
Have you ever done QM/MM? please introduce a free and good package  
for academic user.

Thanks in advance

Farzad Molani,
Ph.D Student,
Department of Theoretical Chemistry and Biochemistry,
K. N. Toosi University of Technology,
Tehran, Iran.
Tel.: 009821 2306 4280
Fax: 009821 2285 3650
Web: http://www.kntu.ac.ir



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Message: 7
Date: Tue, 17 Nov 2009 09:37:28 +
From: "Kukol, Andreas" 
Subject: RE: [gmx-users] access code for qmmm
To: Discussion list for GROMACS users 
Message-ID:
<2f848dc922c8d741bf3a60b7d7108b6a82eecb5...@uh-mailstor.herts.ac.uk>
Content-Type: text/plain; charset="us-ascii"

GROMACS can do QM/MM.

Andreas

---

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org 
] On Behalf Of Farzad Molani

Sent: 17 November 2009 08:57
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] access code for qmmm

Hello,
Have you ever done QM/MM? please introduce a free and good package  
for academic user.

Thanks in advance

Farzad Molani,
Ph.D Student,
Department of Theoretical Chemistry and Biochemistry,
K. N. Toosi University of Technology,
Tehran, Iran.
Tel.: 009821 2306 4280
Fax: 009821 2285 3650
Web: http://www.kntu.ac.ir



--


--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://wwwuser.gwdg.de/~ggroenh/

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[gmx-users] 4. Re: access code for qmmm (Mark Abraham)

[Gerrit Groenhof]

You need a newer version to run ORCA:


   1016:42git clone git://git.gromacs.org/gromacs
   1116:44cd gromacs/
   1216:44git branch --track qmmm origin/qmmm
   1316:44git checkout qmmm
   1416:44git pull


Gerrit

On 21 Nov 2009, at 14:16, gmx-users-requ...@gromacs.org wrote:


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Today's Topics:

  1. Re: amber force field in gromacs (Alan)
  2. Re: amber force field in gromacs (Justin A. Lemkul)
  3. Re: access code for qmmm (Farzad Molani)
  4. Re: access code for qmmm (Mark Abraham)



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[gmx-users] Re: Configuration of Gaussian for QM/MM

[Gerrit Groenhof]

The instruction says:

To find the fortran source file that contains the function you need, you
can use the grep command:

grep -i d1e $GAUSS_DIR/*.F

What is it that you do misunderstand about this?

Gerrit

Is there any misunderstand about instruction ?

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Subject: [gmx-users] [ dummies 2] or [ virtual_sites 2] not works.

[Gerrit Groenhof]

> CYM SG  1   CYM SG  1   0.2 CYS2CYS2
> TRP  N  1   HISH C  1   0.2 TRP HISH
> 
> whdikp.pdb
> REMARK   S  14 x 14 mn oif
> ATOM  1  N   TRP1   -0.813   0.594   1.164
> ATOM  2  H   TRP1   -0.249   1.064   1.843
> ATOM  3  CA  TRP1   -0.264  -0.210   0.004
> ATOM  4  HA  TRP10.855  -0.244   0.066
> ATOM  5  CB  TRP1   -0.633   0.484  -1.321
> ATOM  6  HB1 TRP1   -1.672   0.344  -1.531
> ATOM  7  HB2 TRP1   -0.408   1.528  -1.262
> ATOM  8  CG  TRP10.205  -0.166  -2.397
> ATOM  9  CD1 TRP10.227  -1.464  -2.727
> ATOM 10  HD1 TRP1   -0.407  -2.173  -2.195
> ATOM 11  CD2 TRP11.119   0.455  -3.258
> ATOM 12  NE1 TRP11.166  -1.607  -3.796
> ATOM 13  HE1 TRP1    1.401  -2.473  -4.259
> ATOM 14  CE2 TRP11.673  -0.432  -4.078
> ATOM 15  CE3 TRP11.485   1.803  -3.344
> ATOM 16  HE3 TRP11.065   2.575  -2.699
> ATOM 17  CZ2 TRP12.626  -0.117  -5.054
> ATOM 18  HZ2 TRP13.035  -0.902  -5.690
> ATOM 19  CZ3 TRP12.444   2.145  -4.320
> ATOM 20  HZ3 TRP12.741   3.190  -4.402
> ATOM 21  CH2 TRP12.990   1.222  -5.140
> ATOM 22  HH2 TRP13.727   1.540  -5.878
> ATOM 23  C   TRP1   -0.816  -1.621   0.004
> ATOM 24  O   TRP1   -0.072  -2.712   0.004
> ATOM 25  N   HISH   2   -2.331  -1.621   0.004
> ATOM 26  H   HISH   2   -2.895  -2.093  -0.674
> ATOM 27  CA  HISH   2   -2.881  -0.816   1.162
> ATOM 28  HA  HISH   2   -4.000  -0.781   1.098
> ATOM 29  CB  HISH   2   -2.516  -1.510   2.488
> ATOM 30  HB1 HISH   2   -1.564  -1.990   2.400
> ATOM 31  HB2 HISH   2   -2.494  -0.794   3.283
> ATOM 32  CG  HISH   2   -3.591  -2.538   2.747
> ATOM 33  ND1 HISH   2   -3.867  -3.560   1.846
> ATOM 34  HD1 HISH   2   -3.399  -3.715   0.964
> ATOM 35  CD2 HISH   2   -4.447  -2.700   3.792
> ATOM 36  HD2 HISH   2   -4.608  -2.157   4.723
> ATOM 37  CE1 HISH   2   -4.846  -4.291   2.344
> ATOM 38  HE1 HISH   2   -5.219  -5.152   1.791
> ATOM 39  NE2 HISH   2   -5.203  -3.793   3.502
> ATOM 40  HE2 HISH   2   -5.932  -4.166   4.093
> ATOM 41  C   HISH   2   -2.329   0.595   1.164
> ATOM 42  O   HISH   2   -3.089   1.710   1.164
> 
> Thanks for any suggestions,
> 
> Jose Tusell
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> End of gmx-users Digest, Vol 69, Issue 110
> **

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Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://wwwuser.gwdg.de/~ggroenh/

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[gmx-users] Weird error message from QM/MM run. (yoochan,myung)

[Gerrit Groenhof]

Could you provide more information?
>3. Weird error message from QM/MM run. (yoochan,myung)
>4. Re: Re: Re: Fw: Re: Polymer-protein problem (Mark Abraham)
>5. Re: gas adsorption on CNT (Mark Abraham)
>6. simulation crash with GROMOS96 force field (Vitaly V. Chaban)
>   

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[gmx-users] Re: 1. Need small well known QM/MM example (Ake Sandgren)

[Gerrit Groenhof]

Hi Ake,
you can download two files at 

wwwuser.gwdg.de/~ggroenh/ffamber03.tar.gz and 
wwwuser.gwdg.de/~ggroenh/qmmm_input.tar.gz 

First is the forcefield files (GMXLIB shoul point there)
second is qmmm input files for a QM/MM simulation.

Hope it helps.

Gerrit

> 
> Message: 1
> Date: Thu, 11 Feb 2010 10:05:56 +0100
> From: Ake Sandgren 
> Subject: [gmx-users] Need small well known QM/MM example
> To: gmx-users@gromacs.org
> Message-ID: <1265879156.17090.242.ca...@skalman.hpc2n.umu.se>
> Content-Type: text/plain
> 
> Hi!
> 
> I need a small QM/MM gromacs input data with a well known result (and
> preferably the output too) to compare to the gromacs/gamess-uk setup i'm
> testing.
> 
> Does anyone have something i can use?
> 
> -- 
> Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
> Internet: a...@hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90 7866126
> Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
> 
> 
> 

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[gmx-users] Re: 2. protein in dppc (edmund lee)

[Gerrit Groenhof]

Hi,

If I am allowed to do some advertisement:

you could try the tool g_membed  for inserting proteins as well

http://wwwuser.gwdg.de/~ggroenh/membed.html

Gerrit

gmx-users-requ...@gromacs.org wrote:
>2. protein in dppc (edmund lee)
>
> Date: Tue, 23 Feb 2010 15:55:36 +0800
> From: edmund lee 
> Subject: [gmx-users] protein in dppc
> To: 
> Message-ID: 
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Dear Justin and all..
> I have been struggled for the pass few weeks...I follow the KALP-15 in DPPC 
> tutorials but I am using my own protein instead.
> I had successfully reached the step INFLATEGRO where 2 lipid removed from the 
> upper layer n 2 lipids removed from the lower layer. Then i updated my 
> topology with deducted 4 number of molecule of lipid.
> then I generated the strong_porse.itp using the following command:
> genrestr -f 1_newbox.gro -o strong_posre.itp -fc 10 10 10
> here is how the strong_posre.itp file look like[ position_restraints ];  i 
> funct   fcxfcyfcz   11 10 10 
> 10   21 10 10 10   31 10 
> 10 10   41 10 10 10   51 
> 10 10 1034831 10 10   
>   1034841 10 10 1034851 10 
> 10 1034861 10 10 10
> then i updated the topology (as shown below)
> ; Include Position restraint file#ifdef POSRES#include "posre.itp"#endif
> ; Strong position restraints for InflateGRO#ifdef STRONG_POSRES#include 
> "strong_posre.itp"#endif
> ; Include DPPC chain topology#include "dppc.itp"
> ; Include water topology#include "spc.itp"
> ; System specifications[ system ]128-Lipid DPPC Bilayer 
> [ molecules ]; molecule name nr.DPP124SOL   3655
>
>
>
> and I also add in the "define" line in the energyminimization.mdp file
> here is my em.mdp file 
> define   =-DSTRONG_POSRESintegrator = steepnsteps 
>   = 200constraints= noneemtol
> = 1000.0nstcgsteep= 10 ; do a steep every 10 steps of cgemstep
>  = 0.01 ; used with steepnstcomm  = 1coulombtype  
>   = PMEns_type= gridrlist   = 1.0rcoulomb 
>  = 1.0rvdw = 1.4Tcoupl  = 
> noPcoupl  = nogen_vel= nonstxout  
>= 0 ; write coords every # stepoptimize_fft  = yes
>
> HOWEVER, I get this error when I proceed to the grompp step.
> Fatal error:Syntax error - File strong_posre.itp, line 3Last line read:'[ 
> position_restraints ]'Invalid order for directive position_restraints
> Can anyone guide me in this?Yr comments and advices are appreciated.
> best regards
> edmund  
> _
>   

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[gmx-users] Re: gmx-users Digest, Vol 53, Issue 140: uniform neutralizing plasma for PME (himanshu khandelia)

[Gerrit Groenhof]

Type: text/plain; charset="iso-8859-1"

Is there an implementation in gromacs for using a uniform neutralizing
plasma with PME, to avoid use of counterions?

Thank you

-Himanshu

  


Neutralization is done implicitly, by omitting out the zeroth plane 
wavevector (m=0, see sec. 4.6 of the gmx manual). However, it is 
advisable to use explicit ions always,  as the neutralizing background 
charge leads to artefacts.


BEst,

Gerrit


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[gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with MOPAC7 QM/MM, (Laercio Pol Fachin)

[Gerrit Groenhof]

Today's Topics:


Well, I removed that line, and "make" gone further, but I stopped in other 
error:

---
make[3]: Entrando no diretório `/usr/local/gromacs-4.0.2/src/kernel'
/bin/sh ../../libtool --tag=CC   --mode=link mpicc  -O3 -fomit-frame-pointer 
-finline-functions -Wall -Wno-unused -funroll-all-loops   -o grompp grompp.o 
libgmxpreprocess_mpi.la ../mdlib/libmd_mpi.la ../gmxlib/libgmx_mpi.la  -lxml2 
 -lnsl -lfftw3f -lm   -lSM -lICE -lX11
mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused 
-funroll-all-loops -o grompp grompp.o  ./.libs/libgmxpreprocess_mpi.a 
../mdlib/.libs/libmd_mpi.a ../gmxlib/.libs/libgmx_mpi.a /usr/lib/libxml2.so -lz 
-lnsl -lfftw3f -lm /usr/lib/libSM.so /usr/lib/libICE.so /usr/lib/libX11.so 
/usr/lib/libxcb-xlib.so /usr/lib/libxcb.so /usr/lib/libXau.so 
/usr/lib/libXdmcp.so -ldl
../mdlib/.libs/libmd_mpi.a(qm_mopac.o): In function `call_mopac_SH':
qm_mopac.c:(.text+0x286): undefined reference to `domop_'
../mdlib/.libs/libmd_mpi.a(qm_mopac.o): In function `call_mopac':
qm_mopac.c:(.text+0x83a): undefined reference to `domop_'
../mdlib/.libs/libmd_mpi.a(qm_mopac.o): In function `init_mopac':
qm_mopac.c:(.text+0xc03): undefined reference to `domldt_'
collect2: ld returned 1 exit status
make[3]: ** [grompp] Erro 1
make[3]: Saindo do diretório `/usr/local/gromacs-4.0.2/src/kernel'
make[2]: ** [all-recursive] Erro 1
make[2]: Saindo do diretório `/usr/local/gromacs-4.0.2/src'
make[1]: ** [all] Erro 2
make[1]: Saindo do diretório `/usr/local/gromacs-4.0.2/src'
make: ** [all-recursive] Erro 1
---

Is there something I should do (better, I forgot to do)?
  
Did you use the gromacs adapted mopac sources? If not, please retreive 
them from the website (below).


Alternatively, you seem to have forgotten to set the LIBS to -lmopac and 
LDFLAGS to the location of the mopac library.


Gerrit



Thanks in advance,
Laércio



Message: 2
Date: Tue, 09 Dec 2008 12:26:57 +1100
From: Mark Abraham <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Dificulties compiling Gromacs 4.0.2 with
MOPAC7 QM/MM
To: Discussion list for GROMACS users 
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=UTF-8; format=flowed

Laercio Pol Fachin wrote:
  

Dear GMX users:

I'm facing problems installing Gromacs 4.0.2 with mopac7 QM/MM.

I have downloaded MOPAC7 for SourceForge, as linked in previous mails, 
and installed it. After, MPICH and fftw 3.0.1. So: "./configure 
--enable-mpi --with-qmmm-mopac" runs O.K., but, during


"make":
  

(some shell indications in Portuguese):
---
make[3]: Entrando no diretório `/usr/local/gromacs-4.0.2/src/mdlib'
/bin/sh ../../libtool --tag=CC   --mode=compile mpicc -DHAVE_CONFIG_H 
-I. -I../../src -I/usr/include/libxml2 -I../../include 
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\"   -O3

-fomit-frame-pointer 
  
-finline-functions -Wall-Wno-unused -funroll-all-loops -MT qm_mopac.lo 
-MD -MP -MF .deps/qm_mopac.Tpo -c -o qm_mopac.lo qm_mopac.c
 mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 
-I../../include

-DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3 
  
-fomit-frame-pointer -finline-functions -Wall -Wno-unused 
-funroll-all-loops -MT qm_mopac.lo -MD -MP -MF .deps/qm_mopac.Tpo -c 
qm_mopac.c -o qm_mopac.o

qm_mopac.c:52:17: error: nsb.h: Arquivo ou diretório não encontrado



My Portuguese is not so hot, but I figure this error translates as 
"nsb.h: File or directory not found". That means what it says.
GROMACS 
version 3.3.x had this file, version 4.x doesn't. I had a look at 
qm_mopac.c and I don't think it was using any of the contents of nsb.h, 
so you should be safe to remove this line from qm_mopac.c. Do let us 
know how you get on.


Mark




  Veja quais são os assuntos do momento no Yahoo! +Buscados
http://br.maisbuscados.yahoo.com
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Message: 2
Date: Tue, 9 Dec 2008 23:21:31 +0800
From: "Jinyao Wang" <[EMAIL PROTECTED]>
Subject: [gmx-users] how to compute the solvent density distribution
around  solute and visulize it
To: "gmx-users" 
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain;   charset="gb2312"

gmx-usershello,gmx-users
I would like to compute the solvent density distribution around solute and visualize the solvent density maps around solute. I have read the manual and known the g_densmap could do it. I have carried out the g_densmap as follow, 
g_densmap -f traj.xtc -s topol.tpr -n index.ndx -bin 0.1 -n1 6 -n2 6 -amax 3 -rmax 6 -mirror -unit count -o densmap.xpm

xpm2gs -f densmap.xpm -nice 10 -size 400 -rainbow -o plot.eps

   But the plot.eps is not the figure in the link http://p13.freep.cn/p.aspx?u=v20_p13_p_0812092310359766_0.jpg 
   I want to know more details about how to get the figure in the link. it is appreciated if y

[gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with, MOPAC7 QM/MM

[Gerrit Groenhof]

Ok, but somehow these flags do not show up in the compilation output 
(bit messy copy/paste):



mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
  

-funroll-all-loops -o grompp grompp.o  ./.libs/libgmxpreprocess_mpi.a
../mdlib/.libs/libmd_mpi.a ../gmxlib/.libs/libgmx_mpi.a /usr/lib/libxml2.so -lz
-lnsl -lfftw3f -lm /usr/lib/libSM.so /usr/lib/libICE.so /usr/lib/libX11.so
/usr/lib/libxcb-xlib.so /usr/lib/libxcb.so /usr/lib/libXau.so
/usr/lib/libXdmcp.so -ldl

There should be a -lmopac somewhere then.

Try a make distclean, and reconfigure with the LIBS and LDFLAGS set.

GErrit



--

Message: 4
Date: Thu, 11 Dec 2008 07:54:59 -0800 (PST)
From: Laercio Pol Fachin 
Subject: [gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with
MOPAC7 QM/MM
To: gmx-users@gromacs.org
Message-ID: <554128.85516...@web51510.mail.re2.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Well...

The LDFLAGS and LIBS I have set manually:

LDFLAGS = /usr/local/mopac7-1.10/src/libmopac.a
LIBS = -lxml2  -lnsl -lfftw3f -lmopac -lm   -lSM -lICE -lX11

Probably, I might have confused the correct "gmxmop.f" and "dcart.f" place: 
should them stay in the MOPAC folder with files and objects (mopac7-1.10/src) or in LINUX folder 
with library files (usr/local/lib/)?

Laércio
Message: 2
Date: Thu, 11 Dec 2008 14:51:34 +0100
From: Gerrit Groenhof 
Subject: [gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with
MOPAC7 QM/MM, (Laercio Pol Fachin)
To: gmx-users@gromacs.org
Message-ID: <49411ae6.6020...@gwdg.de>
Content-Type: text/plain; charset=windows-1252; format=flowed


  

Today's Topics:


Well, I removed that line, and "make" gone further, but I


stopped in other error:
  

---
make[3]: Entrando no diretório


`/usr/local/gromacs-4.0.2/src/kernel'
  

/bin/sh ../../libtool --tag=CC   --mode=link mpicc  -O3


-fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loopsÂ
  -o grompp grompp.o libgmxpreprocess_mpi.la ../mdlib/libmd_mpi.la
../gmxlib/libgmx_mpi.la  -lxml2  -lnsl -lfftw3f -lm   -lSM -lICE -lX11
  

mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused


-funroll-all-loops -o grompp grompp.o  ./.libs/libgmxpreprocess_mpi.a
../mdlib/.libs/libmd_mpi.a ../gmxlib/.libs/libgmx_mpi.a /usr/lib/libxml2.so -lz
-lnsl -lfftw3f -lm /usr/lib/libSM.so /usr/lib/libICE.so /usr/lib/libX11.so
/usr/lib/libxcb-xlib.so /usr/lib/libxcb.so /usr/lib/libXau.so
/usr/lib/libXdmcp.so -ldl
  

../mdlib/.libs/libmd_mpi.a(qm_mopac.o): In function `call_mopac_SH':
qm_mopac.c:(.text+0x286): undefined reference to `domop_'
../mdlib/.libs/libmd_mpi.a(qm_mopac.o): In function `call_mopac':
qm_mopac.c:(.text+0x83a): undefined reference to `domop_'
../mdlib/.libs/libmd_mpi.a(qm_mopac.o): In function `init_mopac':
qm_mopac.c:(.text+0xc03): undefined reference to `domldt_'
collect2: ld returned 1 exit status
make[3]: ** [grompp] Erro 1
make[3]: Saindo do diretório `/usr/local/gromacs-4.0.2/src/kernel'
make[2]: ** [all-recursive] Erro 1
make[2]: Saindo do diretório `/usr/local/gromacs-4.0.2/src'
make[1]: ** [all] Erro 2
make[1]: Saindo do diretório `/usr/local/gromacs-4.0.2/src'
make: ** [all-recursive] Erro 1
---

Is there something I should do (better, I forgot to do)?
  

Did you use the gromacs adapted mopac sources? If not, please retreive 
them from the website (below).


Alternatively, you seem to have forgotten to set the LIBS to -lmopac and 
LDFLAGS to the location of the mopac library.


Gerrit


  

Thanks in advance,
Laércio



Message: 2
Date: Tue, 09 Dec 2008 12:26:57 +1100
From: Mark Abraham 
Subject: Re: [gmx-users] Dificulties compiling Gromacs 4.0.2 with
MOPAC7 QM/MM
To: Discussion list for GROMACS users 
Message-ID: <493dc961.4000...@anu.edu.au>
Content-Type: text/plain; charset=UTF-8; format=flowed

Laercio Pol Fachin wrote:
  


Dear GMX users:

I'm facing problems installing Gromacs 4.0.2 with mopac7 QM/MM.

I have downloaded MOPAC7 for SourceForge, as linked in previous mails,
  


  
and installed it. After, MPICH and fftw 3.0.1. So: "./configure 
--enable-mpi --with-qmmm-mopac" runs O.K., but, during

  

"make":
  


(some shell indications in Portuguese):
---
make[3]: Entrando no diretório
  

`/usr/local/gromacs-4.0.2/src/mdlib'
  
/bin/sh ../../libtool --tag=CC   --mode=compile mpicc -DHAVE_CONFIG_H 
-I. -I../../src -I/usr/include/libxml2 -I../../include 
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\"   -O3

  
-fomit-frame-pointer 
  


-finline-functions -Wall-Wno-unused -funroll-all-loops -MT qm_mopac.lo
  


  

-MD -MP -MF .deps/qm_mopac.Tpo -c -o qm_mopac.lo qm_mopac.c
 mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 
-I../../include

  
-DGMXLIBDIR=\&qu

[gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with MOPAC7 QM/MM, (Laercio Pol Fachin

[Gerrit Groenhof]

gmx-users-requ...@gromacs.org wrote:

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Today's Topics:

   1. RE: Subject: Re: Re: [gmx-users] Gromacs 4 bug? (Berk Hess)
   2. Re: Dificulties compiling Gromacs 4.0.2 with MOPAC7   QM/MM
  (Laercio Pol Fachin)

  
  


How was the mopac library compiled? You might have to link also to -lg2c?

Gerrit


Message: 2
Date: Mon, 15 Dec 2008 03:40:53 -0800 (PST)
From: Laercio Pol Fachin 
Subject: [gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with
MOPAC7  QM/MM
To: gmx-users@gromacs.org
Message-ID: <627734.45704...@web51508.mail.re2.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi!

Now, I tried to configure Mopac QMMM not manually, that is:

"./configure --enable-mpi --with-qmmm-mopac CPPFLAGS=-DUSE_MOPAC LIBS=-lmopac 
LDFLAGS=-L/usr/local/mopac7-1.10/src"

It ran O.K., but I had other problem now:

---

ranlib .libs/libgmxpreprocess_mpi.a
creating libgmxpreprocess_mpi.la
(cd .libs && rm -f libgmxpreprocess_mpi.la && ln -s ../libgmxpreprocess_mpi.la 
libgmxpreprocess_mpi.la)
mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include 
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -DUSE_MOPACÂ  -O3 
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT grompp.o 
-MD -MP -MF .deps/grompp.Tpo -c -o grompp.o grompp.c
mv -f .deps/grompp.Tpo .deps/grompp.Po
/bin/sh ../../libtool --tag=CC   --mode=link mpicc  -O3 -fomit-frame-pointer 
-finline-functions -Wall -Wno-unused -funroll-all-loops  
-L/usr/local/mopac7-1.10/src   -o grompp grompp.o libgmxpreprocess_mpi.la 
../mdlib/libmd_mpi.la ../gmxlib/libgmx_mpi.la  -lxml2  -lnsl -lfftw3f -lm 
-lmopac  -lSM -lICE -lX11
mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused 
-funroll-all-loops -o grompp grompp.o  -L/usr/local/mopac7-1.10/src 
./.libs/libgmxpreprocess_mpi.a ../mdlib/.libs/libmd_mpi.a 
../gmxlib/.libs/libgmx_mpi.a /usr/lib/libxml2.so -lz -lnsl -lfftw3f -lm -lmopac 
/usr/lib/libSM.so /usr/lib/libICE.so /usr/lib/libX11.so /usr/lib/libxcb-xlib.so 
/usr/lib/libxcb.so /usr/lib/libXau.so /usr/lib/libXdmcp.so -ldl
/usr/local/mopac7-1.10/src/libmopac.a(lread.o): In function `e_rsle':
(.text+0x160): undefined reference to `__ctype_b'
/usr/local/mopac7-1.10/src/libmopac.a(lread.o): In function `e_rsle':
(.text+0x21f): undefined reference to `__ctype_b'
/usr/local/mopac7-1.10/src/libmopac.a(lread.o): In function `e_rsle':
(.text+0x296): undefined reference to `__ctype_b'
/usr/local/mopac7-1.10/src/libmopac.a(lread.o): In function `e_rsle':
(.text+0x2d0): undefined reference to `__ctype_b'
/usr/local/mopac7-1.10/src/libmopac.a(lread.o): In function `e_rsle':
(.text+0x8b2): undefined reference to `__ctype_b'
/usr/local/mopac7-1.10/src/libmopac.a(lread.o):(.text+0xb05): more undefined 
references to `__ctype_b' follow
collect2: ld returned 1 exit status
make[3]: ** [grompp] Erro 1
make[3]: Saindo do diretório `/usr/local/gromacs-4.0.2/src/kernel'
make[2]: ** [all-recursive] Erro 1
make[2]: Saindo do diretório `/usr/local/gromacs-4.0.2/src'
make[1]: ** [all] Erro 2
make[1]: Saindo do diretório `/usr/local/gromacs-4.0.2/src'
make: ** [all-recursive] Erro 1

---

I tried it with both Gromacs 4.0.2 and 3.3.3, and the same output error 
appears; so, probably, it's something I forgot... Any idea?

Laércio


Message: 4
Date: Fri, 12 Dec 2008 10:18:20 +0100
From: Gerrit Groenhof 
Subject: [gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with,
MOPAC7 QM/MM
To: gmx-users@gromacs.org
Message-ID: <49422c5c.2060...@gwdg.de>
Content-Type: text/plain; charset=windows-1252; format=flowed

Ok, but somehow these flags do not show up in the compilation output 
(bit messy copy/paste):


  

mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
  


-funroll-all-loops -o grompp grompp.o  ./.libs/libgmxpreprocess_mpi.a
../mdlib/.libs/libmd_mpi.a ../gmxlib/.libs/libgmx_mpi.a /usr/lib/libxml2.so -lz
-lnsl -lfftw3f -lm /usr/lib/libSM.so /usr/lib/libICE.so /usr/lib/libX11.so
/usr/lib/libxcb-xlib.so /usr/lib/libxcb.so /usr/lib/libXau.so
/usr/lib/libXdmcp.so -ldl

There should be a -lmopac somewhere then.

Try a make distclean, and reconfigure with the LIBS and LDFLAGS set.

GErrit

  

--

Message: 4
Date: Thu, 11 Dec 2008 07:54:59 -0800 (PST)
From: Laercio Pol Fachin 
Subject: [gmx-users] Re: Dificulties 

Subject: [gmx-users] gromacs QM/MM

[Gerrit Groenhof]

Although there is not much interface specific information, you can check 
one of our recent papers, eg.  L.V. Schaefer et al., PLoS computational 
biology, 4 (2008), e134.


More information on how to build up the interface on the gaussian side 
you find on wwwuser.gwdg.de/~ggroenh


Gerrit


---

Message: 3
Date: Wed, 18 Feb 2009 12:12:12 +0100 (CET)
From: "Jacopo Sgrignani" 
Subject: [gmx-users] gromacs QM/MM
To: gmx-users@gromacs.org
Message-ID:
<4583.79.44.176.168.1234955532.squir...@alpha.cerm.unifi.it>
Content-Type: text/plain;charset=iso-8859-1

Hi
I would like to use the gromacs/Gaussian03 interface and i would like to
know if there are any papers with data obtained using this interface.

Thanks a lot

Jacopo



  



  


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[gmx-users] Re: Positive energy for Coulumb term. Does this mean Coulumb, interaction destabilizes protein? (Seungpyo Hong)

[Gerrit Groenhof]

Coulomb 1-4 is only beteen the atoms that are 3 bonds away from each 
other. The bonds prevent these atoms to get apart too far, so 1-4 won't 
destabilize the overall structure. The SR part is negative, thus keeping 
your protein together.


Gerrit




Message: 3
Date: Fri, 6 Mar 2009 19:43:19 +0900
From: Seungpyo Hong 
Subject: [gmx-users] Positive energy for Coulumb term. Does this mean
Coulumb interaction destabilizes protein?
To: gmx-users@gromacs.org
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

Dear GMX-Users,

As I analyze energy terms of proteins, I found something looks weird.
I thought that fullly folded proteins are stabilized by Coulomb interaction
(such as hydrogen bonds).
However, what I found embarasses me.

The Coulomb interaction seems to destabilize the protein structure as its
energy is positive.

Coul-SR + Coul-14 = 32 > 0
Coul-SR + Coul-14 + Coul-SR(Protein-Non-Protein) = 18 > 0


Energy  Average   RMSD Fluct.  Drift
Tot-Drift
---
Coul-SR:Protein-Protein-11.6253365.244357.507  -0.735925
-259.047
LJ-SR:Protein-Protein  -6.51389204.554203.627   0.191426
67.3824
Coul-14:Protein-Protein 38.58481212.261196.751.90253
669.696
LJ-14:Protein-Protein   3.58465112.688112.645 -0.0303438
-10.6811
Coul-SR:Protein-Non-Protein   -14.1247443.927437.195   -0.75795
-266.8
LJ-SR:Protein-Non-Protein   -1.5147147.692446.2568   -0.11429
-40.2302


I thought of the total charge of the protein; but it is only +2.
And, the structure is quite stable through the simulation. (RMSD: 0.17)

I am quite confusing about the effect of Coulumb interaction on the
stability of the protein.
I feel like I am missing very important concept about the stability of
protein or the energy term used here.
Can anyone help me to understand the effect of Coulumb interaction in the
stability of the protein?

Any opinion or comment would be great help for me.

Thank you very much!

Sincerely,
Seungpyo Hong

  


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[gmx-users] open positions

[Gerrit Groenhof]

Dear all,

I would greatly appreciate if you could bring this to the attention of
those who might be interested.

The computational biomolecular chemistry group at the
Max-Planck-Institute for Biophysical Chemistry in Goettingen, Germany,
is currently looking for phd students and postdocs, who are interested
in applying computer simulation to discover the mechanisms of
biochemical processes. Please visit our website for more information
(http://wwwuser.gwdg.de/~ggroenh/).

The group's main objective is to acquire a detailed understanding of
how proteins regulate chemical reactions, and, in collaboration with
experimental partners, to use these insights to create new devices
that can mimic biological function.

In one of the projects we use computer simulations to design mutants
of photoactive proteins that alter the original function. As a proof
of principle we will first try to changing a photoreceptor, such as
retinal, into a fluorescent protein. In additon we will also focus on
artificial devices that can convert light to action.

In the simulations, quantum mechanics (QM) is used to model electronic
rearrangements in those parts of the system involved in the
reaction. For the remainder, typically consisting of the apoprotein
and the solvent, a simple forcefield model (MM) suffices. QM/MM
gradients are computed at every step of the MD simulation. We have
demonstrated the validity of hybrid QM/MM approaches for
photobiological reactions in recent applications on photoactivation of
photoreceptor proteins, on photo-switching of fluorescent proteins and
on benign and malign photochemical reactions in DNA.

We are looking for motivated candidates with a background in physics
or physical chemistry, who are interested in biological chemistry. Any
experience with quantum chemistry, molecular dynamics, and/or computer
programming would be great.

If you are interested in joining our group, please send a short
motivation letter and a cv with contact details of one or two
references, preferably by email, to ggro...@gwdg.de.

Kind regards,

Gerrit

--

Gerrit Groenhof
Biomolecular computional chemistry
Max-Planck-Institute for Biophysical Chemistry,
D-37077 Goettingen
Germany
tel. +49(0)551-2012321
fax. +49(0)551-2012302
http://wwwuser.gwdg.de/~ggroenh/
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[gmx-users] Re: gmx-users] Mopac7 / Gromacs 4.0.4 Issue

[Gerrit Groenhof]

Hi, 


it should suffice to set the LIBS prior to compiling.

With what compiler was mopac7 compiled? 


I have thus far only been able to compile a working version with f2c/gcc.

Not optimal. Using the intel fortran compiler, I also get a running mopac, but 
the results are not correct and I don't know why.

Anyway, after creating the library, I set LIBS '-lmopac -lf2c -lm', and 
configure creates working makefiles.

Hope this helps.

Gerrit


Message: 3
Date: Wed, 8 Apr 2009 16:24:34 -0700
From: Matthew Lardy 
Subject: [gmx-users] Mopac7 / Gromacs 4.0.4 Issues
To: gmx-users@gromacs.org
Message-ID:
<12741c010904081624s46a146d3kbf3519f600594...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi all,
I have been playing with Mopac7 (both version 7 and the more recent Mopac
7-1.10 release).  I have compiled both Mopac and
Gromacs independently without issue.  But when I try to add -with-qmmm-mopac
to my ./configure line, I am unable to compile and link them together.

I have been looking at this for some time, and I have read the posts to this
list.  I have two issues that I think may be related.

First, when I add the -lmopac to the LIBS environment variable, -DUSE_MOPAC
to CPPFLAGS and -L/(Path to Mopac Libs) to LDFLAGS, I don't make it out of
the configure alive:

from config.log
ld: -lmopac

So, I added the lmopac information in to pkgconfig...  Once again no dice
with ./configure.So I then reset my environment and stepped through the
configure.  Now after removing the references to mopac in my environment,
run the ./configure as I have done so previously, and then add the mopac
environment variables by hand, I get the following errors:

icc -O3 -tpp6 -axK -ip -w -funroll-all-loops -o grompp grompp.o
-L/path/to/fftw-3.2.optim-thread/lib -L/vscrn/Packages/MopacOpt/lib
./.libs/libgmxpreprocess.a ../mdlib/.libs/libmd.a
/path/to/gromacs-4.0.4/src/gmxlib/.libs/libgmx.a ../gmxlib/.libs/libgmx.a
-lnsl /path/to/fftw-3.2.optim-thread/lib/libfftw3f.a -lm -lmopac
/path/to/MopacOpt/lib/libmopac.a(lread.o)(.text+0x160): In function
`e_rsle':
: undefined reference to `__ctype_b'
/path/to/MopacOpt/lib/libmopac.a(lread.o)(.text+0x21f): In function
`e_rsle':
: undefined reference to `__ctype_b'
/path/to/MopacOpt/lib/libmopac.a(lread.o)(.text+0x296): In function
`e_rsle':
: undefined reference to `__ctype_b'
/path/to/MopacOpt/lib/libmopac.a(lread.o)(.text+0x2d0): In function
`e_rsle':
: undefined reference to `__ctype_b'
/path/to/MopacOpt/lib/libmopac.a(lread.o)(.text+0x8b2): In function
`e_rsle':
: undefined reference to `__ctype_b'
/path/to/MopacOpt/lib/libmopac.a(lread.o)(.text+0xb05): more undefined
references to `__ctype_b' follow
make[3]: *** [grompp] Error 1
make[3]: Leaving directory `/path/to/gromacs-4.0.4/src/kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/path/to/gromacs-4.0.4/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/path/to/gromacs-4.0.4/src'
make: *** [all-recursive] Error 1

I should add that I have downloaded and used Gerrit's mopac library, as well
as patched a clean version of Mopac7.  No dice.  Oh yeah, I have tried the
GNU compilers as well.  And, cleaned the application every time I have tried
to rebuild.

I figure that there is something simple that I have forgotten.

Thanks in advance!
Matthew


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Re: [gmx-users] How to obtain a approperiate PDB file of DNA?

[Gerrit Groenhof]

Check the program Biomer. I allows you to create any type of DNA  
molecule: http://casegroup.rutgers.edu/Biomer/index.html


You will also need the amber forcefield for DNA.

Gerrit


Message: 7
Date: Fri, 10 Apr 2009 12:21:33 +0800
From: li ming 
Subject: Re: [gmx-users] How to obtain a approperiate PDB file of DNA?
To: Discussion list for GROMACS users 
Message-ID:
<114aa2a90904092121m58c2eceaq42ce8731c9aa...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi, Mark:

I want to check the chain length of DNA on the translocation time  
through a

nanopore. So the DNA chains with different polymerization but the same
monomer structure is necessary. How can I solve this problem?

Does anybody has a optimized DNA pdb file for GMX simulation?

Thanks a lot!!

Ming

2009/4/10 Mark Abraham 


li ming wrote:


Hi, all...
I have a question on the pdb files of DNA:
How can I obtain an appropriate DNA pdb file for GMX simulation? I  
just
download some pdb files from Internet, but it is not compatible  
for GMX,
saying that the residue was not found in rtp file. How can I solve  
this

problem? Are the references available on this problem?



Perhaps you should start by searching for some tutorial material with
emphasis on these types of simulation.

Furthermore, if I want to get several DNA pdb files with increasing  
degree
of polymerization (such as 10, 20, 50 etc.). How can I achieve  
this goal?




This may or may not be easy to achieve, but you should start by  
describing
it more fully. What are you wanting to polymerize, and what do you  
mean by

that word?

Mark
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--
Ming Li
Institute of Chemistry,Chinese Academy of Sciences
Zhongguancun, Beijing, 100080, P. R. China
Tel: +86-10-13811601014 / 62564829
E-mail: lim...@iccas.ac.cn / mingli1...@gmail.com
...
Knowledge is a city to the building of which every human being  
brought a

stone.
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End of gmx-users Digest, Vol 60, Issue 65
*****


--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://wwwuser.gwdg.de/~ggroenh/

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Re: [gmx-users] Avoiding parameterization step

[Gerrit Groenhof]

Hi All User,

I have been wondering whether it is advisable to avoid parametrization step by 
freezing the atoms in MD
simulation.
  

Depends on what you want to do.

You most likely would still need the charge distribution, which is the 
most difficult part of the parametrization part usually.

Bonded interactions can often be guessed by comparing to known residues.

Gerrit
With regards, 
Abu 



  


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Re: [gmx-users] Avoiding parameterization step

[Gerrit Groenhof]

Thank you very much for your response. I am at the moment interested in doing 
conformational search.
  


Using freeze groups in combination with conformational search does not 
seem optimal...



Is there any good paper that explain nicely about doing the charge distribution 
calculation?
  
You need to do an ab initio calculation on the system you want to 
parametrize. This will give you the true charge distribution to which 
you can fit a set of partial charges located on the nuclei. There are 
several possibilities to do the fitting, check what the QM programs you 
can use support. But in the end the charges are not too strongly 
dependent on the fitting/level of QM. In addition you can sample several 
configurations and use some sort of averaging to get the partial charge 
(see RESP).


Gerrit


With regards,
Abu 

  

Date: Tue, 11 Mar 2008 10:16:51 +0100
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Avoiding parameterization step




Hi All User,

I have been wondering whether it is advisable to avoid parametrization step by 
freezing the atoms in MD
simulation.
  
  

Depends on what you want to do.

 You most likely would still need the charge distribution, which is the 
most difficult part of the parametrization part usually.

 Bonded interactions can often be guessed by comparing to known residues.

Gerrit

With regards, 
Abu 



  
  

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Re: [gmx-users] atomname -> atomic number

[Gerrit Groenhof]

Hi,

I would like to write a reader for *.gro files, but I couldn't find any
information about how to map the atomname to the atomic number. Can
anyone shed some light on this problem? I would be most grateful.
  


The ff*nb.itp file contains already the atomic numbers of the atoms. 
Probably not too easy to use directly.


These numbers are read in, and you could even think of writing a small 
tool from the template source code that writes out atomnumber and 
coordinates. After reading tpr file, atomnumber are stored in 
t_mdatoms->atomicnumber (include/types/mdatom.h).

BEst,
Gerrit



Cheers,
Daniel



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Re: [gmx-users] QM/MM compilation

[Gerrit Groenhof]

Message: 3
Date: Tue, 20 May 2008 18:59:58 +0200
From: Ran Friedman <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] QM/MM compilation
To: Discussion list for GROMACS users 
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1

Dear Gerrit,

Hitch-hiking with a related issue. I  saw on your presentation for the
Stanford workshop that GMX can work with DFTB. Is this just planned?

Ran.

  

Hi Ran,

It is implemented, but not in the 3.3.3 release yet.
If you are interested, I can make a patch or somehting.

Gerrit
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[gmx-users] Re: forward and reverse free energy not consistant (Li Qiang)

[Gerrit Groenhof]

Looks like hysteresis. Do you do slow growth, or discrete FEP?

Gerrit




Dear all Gmxers,

I am calculating a mutation free energy from L<->A for a five AA 
peptides using G96 53a6 force field.

however, my dG_for and dG_rev is quite different.
dG_for(lambda=0.00) = - 9.9 kJ/mol
dG_rev(lambda=1.00) =   1.33 kJ/mol

Is there anything wrong with setting up topologies?

Here is the [atoms] part for morphed atoms. and I attached the full .top 
in the attachment.

For L->A:
[ atoms ]
17CH2  2LEU CB  6  0 14.027  
CH3   0   15.035; qtot 1
18CH1  2LEU CG  7  0 13.019  
DUM   0   13.019; qtot 1
19CH3  2LEUCD1  7  0 15.035  
DUM   0   15.035; qtot 1
20CH3  2LEUCD2  7  0 15.035  
DUM   0   15.035; qtot 1



For A->L :
[ atoms ]
17CH3  2ALA CB  6  0 15.035  
CH2014.027; qtot 1
60DUM  6DUMDUM 24  013.019  
CH1013.019
61DUM  6DUMDUM 24  015.035  
CH3015.035
62DUM  6DUMDUM 24  015.035  
CH3015.035


thanks for help

LQ
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[gmx-users] Re: QMMM memory problem

[Gerrit Groenhof]

Was gromacs configured with the --with-qmmm-gaussian option?

Is gaussian installed and running as well?

can you make a tar file of the input files (topology, index, mdp, 
configuration) and send it directly to me (i.e not via userlist)?


Gerrit




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Message: 2
Date: Thu, 3 Jul 2008 13:37:42 -0700 (PDT)
From: Alcides Nicastro <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Re: QMMM memory problem
To: Discussion list for GROMACS users 
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="utf-8"

Yes. The system is a methane molecule with 30 waters (from spc). There are 
about 95 atoms. The QM subsystem is the methane. The GROMACS version is 3.3.1 
and it was instaled (in single precision) in an AMD Athlon64 with Fedora Core 5 
and 1.5 Gb RAM.
The options in .mpd file are:

QMMMÂ Â Â  Â Â Â  = yes
QMMM-grps    = ME
QMMMscheme    = normal
QMmethod    = RHF
QMbasis        = STO-3G
QMcharge    = 0

Thanks,
Alcides


  


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[gmx-users] compilation problem with mopac in gromacs 3.3.3, and x86_64 machine

[Gerrit Groenhof]

Message: 1
Date: Tue, 8 Jul 2008 10:18:30 +
From: Abu Naser <[EMAIL PROTECTED]>
Subject: [gmx-users] compilation problem with mopac in gromacs 3.3.3
and x86_64 machine
To: 
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"


Hi Gerrit,

I am having problem  during compilation as :

/mdlib/.libs/libmd_d.a(qm_mopac.o): In function `call_mopac_SH':
qm_mopac.c:(.text+0x2fc): undefined reference to `domop_'
../mdlib/.libs/libmd_d.a(qm_mopac.o): In function `call_mopac':
qm_mopac.c:(.text+0x831): undefined reference to `domop_'
../mdlib/.libs/libmd_d.a(qm_mopac.o): In function `init_mopac':
qm_mopac.c:(.text+0xace): undefined reference to `domldt_'
collect2: ld returned 1 exit status

Can you please give a clue why this is happening?

with regards,
Abu




  
It is either what Nizamov suggests, or yoy do not have a working mopac 
library. Did you compile a working stand-alone mopac executable before 
creating the library?


There is another issue I had with 64 bit machines. The code does not 
give the correct resutls when compiled in 64 bit mode. I have not found 
out why yet.  In the end we had to create static mdrun binary on 32 bit 
machine.


Gerrit


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Re: [gmx-users] CPMD- QM MM simulation

[Gerrit Groenhof]

Message: 1

Date: Fri, 5 Sep 2008 15:48:12 -0700
From: "Chih-Ying Lin" <[EMAIL PROTECTED]>
Subject: [gmx-users] CPMD- QM MM simulation
To: gmx-users@gromacs.org
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"

Hi
I read some papers, which the authors use CPMD - QM MM simulation
to reparametrize the force field parameters.

But, they did not say the details.
Could anyone explain this more here?
  

Why don't you contact the authors?

Gerrit


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[gmx-users] Re: Compile gromacs 4.0.7 with mopac (Stefan Hoorman)

[Gerrit Groenhof]

> 
> 
>  1. Re: Non-conservation of total energy while using structure
> file to resume the simulation (Mark Abraham)
>  2. Compile gromacs 4.0.7 with mopac (Stefan Hoorman)

Try linking with g2c.
Best wishes,

Gerrit


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Re: Subject: [gmx-users] error compiling mopac and gromacs

[Gerrit Groenhof]

Depending on how your libmopac.a was biuld, you need the to include the f2c or 
g2c library as well.

Gerrit



> Message: 5
> Date: Sat, 12 Jun 2010 14:33:02 +0530 (IST)
> From: subarna thakur 
> Subject: [gmx-users] error compiling  mopac and gromacs
> To: gmx-users@gromacs.org
> Message-ID: <371899.78968...@web95516.mail.in.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi 
> I am trying to link mopac with gromacs in a 32 bit linux machine. I have 
> downloaded the libmopac.a file and kept it under /usr/local/lib. I installed 
> fftw with double precision and then I set the enviornmental variables for 
> linking mopac and gromacs 
> export LDFLAGS="-L/usr/local/lib  -Wl,--wrap,__ctype_b"
> export CPPFLAGS="/usr/local/include -DUSE_MOPAC"
> export LIBS="lmopac
> 
> then I have ran the ./configure --with-qmmm-mopac --disable-float.It seems to 
> run ok.Then I used the make command but an error is comming as follows-
> /usr/local/lib/libmopac.a(lread.o)(.text+0x160): In function `e_rsle':
> : undefined reference to `__wrap___ctype_b'
> /usr/local/lib/libmopac.a(lread.o)(.text+0x21f): In function `e_rsle':
> : undefined reference to `__wrap___ctype_b'
> /usr/local/lib/libmopac.a(lread.o)(.text+0x296): In function `e_rsle':
> : undefined reference to `__wrap___ctype_b'
> /usr/local/lib/libmopac.a(lread.o)(.text+0x2d0): In function `e_rsle':
> : undefined reference to `__wrap___ctype_b'
> /usr/local/lib/libmopac.a(lread.o)(.text+0x8b2): In function `e_rsle':
> : undefined reference to `__wrap___ctype_b'
> /usr/local/lib/libmopac.a(lread.o)(.text+0xb05): more undefined references to 
> `__wrap___ctype_b' follow
> collect2: ld returned 1 exit status
> make[3]: *** [grompp] Error 1
> make[3]: Leaving directory `/usr/gromacs-4.0.3/src/kernel'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/usr/gromacs-4.0.3/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/usr/gromacs-4.0.3/src'
> make: *** [all-recursive] Error 1
>  
> Please suggest where I have gone wrong.
>  Subarna Thakur
> 
> 
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Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://wwwuser.gwdg.de/~ggroenh/

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[gmx-users] Re: gmx-users Digest, Vol 74, Issue 183

[Gerrit Groenhof]

ology. Using mult=3
> Dihedral around 820,838 not found in topology. Using mult=3
> Dihedral around 842,852 not found in topology. Using mult=3
> Dihedral around 856,876 not found in topology. Using mult=3
> Dihedral around 880,896 not found in topology. Using mult=3
> Dihedral around 900,913 not found in topology. Using mult=3
> Dihedral around 917,927 not found in topology. Using mult=3
> Dihedral around 931,951 not found in topology. Using mult=3
> Dihedral around 955,975 not found in topology. Using mult=3
> Dihedral around 979,985 not found in topology. Using mult=3
> Dihedral around 989,1007 not found in topology. Using mult=3
> Dihedral around 1011,1031 not found in topology. Using mult=3
> Dihedral around 1035,1055 not found in topology. Using mult=3
> Dihedral around 1059,1079 not found in topology. Using mult=3
> Dihedral around 1083,1090 not found in topology. Using mult=3
> Dihedral around 1094,1097 not found in topology. Using mult=3
> Dihedral around 1109, not found in topology. Using mult=3
> Dihedral around 1115,1122 not found in topology. Using mult=3
> Dihedral around 1126,1133 not found in topology. Using mult=3
> 
> is this rama.xvg file true and intact?
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http://wwwuser.gwdg.de/~ggroenh/

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[gmx-users] Re: eg compilation problem in Mopac gromacs (vidhya sankar)

[Gerrit Groenhof]

> 
>> *From:* gmx-users-boun...@gromacs.org [mailto:
>> gmx-users-boun...@gromacs.org] *On Behalf Of *Sai Pooja
>> *Sent:* Wednesday, 8 September 2010 3:18 PM
>> *To:* Discussion list for GROMACS users
>> *Subject:* [gmx-users] Alanine dipeptide simulations
>> 
>> 
>> 
>> Hi,
>> 
>> 
>> I am running an npt simulation on alanine dipeptide in explicit solvent
>> using charmm forcefield and tip3p.
>> 
>> The pressure is set to 1bar and the barostat is Parrinello-Rahman. The
>> simulation has been running for 45 ns and has not achieved the target
>> average pressure of 1 bar.
>> 
>> I don;t understand why is this the case.
>> 
>> My mdp file:
>> 
>> ; RUN CONTROL PARAMETERS
>> integrator   = md
>> dt   = 0.002
>> nsteps   = 50
>> 
>> ; OUTPUT CONTROL OPTIONS
>> nstxout  = 0; No output, except for
>> last frame (coordinates)
>> nstvout  = 0; No output, except for
>> last frame (velocities)
>> nstfout  = 0; No output, except for
>> last frame (forces)
>> nstlog   = 5000; Write every step to the
>> log
>> nstenergy= 5000; Write energies at
>> every step
>> xtc_grps = Protein SOL
>> nstxtcout= 5000; Do not write a
>> compressed trajectory
>> energygrps   = Protein SOL  ; Write energy information
>> separately for these groups
>> 
>> ; NEIGHBORSEARCHING PARAMETERS
>> nstlist  = 5
>> ns-type  = Grid
>> pbc  = xyz
>> rlist= 0.9
>> 
>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>> coulombtype  = PME
>> fourierspacing   = 0.15
>> rcoulomb = 0.9
>> vdw-type = Cut-off
>> rvdw = 1.0
>> 
>> ; FFT grid size, when a value is 0 fourierspacing will be used =
>> fourier_nx   = 0
>> fourier_ny   = 0
>> fourier_nz   = 0
>> ; EWALD/PME/PPPM parameters =
>> pme_order= 4
>> ewald_rtol   = 1e-05
>> epsilon_surface  = 0
>> optimize_fft = no
>> ; Temperature coupling
>> tcoupl   = nose-hoover
>> tc-grps  = Protein  Non-Protein
>> tau_t= 0.2  0.2
>> ref_t= 300  300
>> 
>> ; Pressure coupling
>> Pcoupl   = Parrinello-Rahman
>> Pcoupltype   = Isotropic
>> tau_p= 1.0
>> compressibility  = 4.5e-5
>> ref_p= 1.0
>> 
>> ; OPTIONS FOR BONDS
>> constraints  = all-bonds
>> 
>> 
>> Pooja
>> 
>> 
>> 
>> 
>> --
>> Quaerendo Invenietis-Seek and you shall discover.
>> 
>> --
>> gmx-users mailing listgmx-users@gromacs.org
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> 
> 
> 
> -- 
> Quaerendo Invenietis-Seek and you shall discover.
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> End of gmx-users Digest, Vol 77, Issue 45
> *

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Gerrit Groenhof
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Goettingen
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http://wwwuser.gwdg.de/~ggroenh/

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Re: [Fwd: Re: [gmx-users] QMMM free energy]

[Gerrit Groenhof]

Hi Fiske,

From what I understand, you want to compute the free energy for 
changing one or more atoms in the QM subsystem. I never considered doing 
this because I do not expect to get sufficient sampling. But in my 
opinion this should be possible.


In case only atoms in the QM subsystem change it is straightforward. But 
I might overlook something important (maybe someone can comment on this 
if I make a mistake).


I think you should modify the code, so that there are two QM/MM 
computations per step. Once in the A state and once in the B state, 
which gives VA and VB. From that you can compute
V(lambda) = lamda VB + (1-lambda) VA. And dv/dl = VB-VA. This is then 
the QM and coulombic QM/MM contribution to dv/dlambda. The lennerd jones 
should work automatically.


But this works only if you are not modifying the charges of the MM 
atoms. Then things get more messy.


However, there is a problem with neighbour searching. Right now, the 
QM/MM neighbour list is constructed only in the

if (!bFreeEnergy)
branch of the put_in_list function. I think this is why mdrun crashes. 
the qmmm interface expects to find MM neighbours, but the QMMM nblists 
are not created.

You can copy the if(bQMMM) branch into the free energy branch.

Best,

Gerrit







Subject:
Re: [gmx-users] QMMM free energy
From:
Erik Lindahl <[EMAIL PROTECTED]>
Date:
Wed, 30 May 2007 17:34:59 +0200
To:
Discussion list for GROMACS users 

To:
Discussion list for GROMACS users 


Hi,

I'm not a QM expert myself (Gerrit, comments?),  but I'm pretty sure 
the main reason is that you cannot either mutate atom types or 
decouple interactions gradually in the QM part of the system. Once 
this is solved for a pure QM system it should be straightforward to 
implement the QM/MM interface of it.


Cheers,

Erik

On May 30, 2007, at 5:30 PM, Robert fiske wrote:

With the original QM/MM implementation, free energy is currently not 
possible (yet). From what you report, I guess that also with the 
CPMD interface it does not work.


The CPMD interface is mostly plugged into the same setup as the other 
QM interfaces, I was able to bypass the error by copying modifying 
the free energy else statement to bypass the vdw calculations for the 
case of bQMMM true (and generally try to have that code match the 
bQMMM case of non free energy runs).  But since my background is 
Computer Engineering and not chemistry (Chemistry 101 is as far as I 
got in formal training)  I don't really know what should be done (I 
assume since as you said it's not implemented yet although I don't 
get a run time error that the results will be off).


Are QM/MM free energy calculations substantially different than MM 
calculations, or is it just not implemented because no one has needed 
to do QM/MM with free energy yet?



fiske
Gogonea Group
Cleveland State University

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Subject:
Re: [gmx-users] QMMM free energy
From:
"Robert fiske" <[EMAIL PROTECTED]>
Date:
Wed, 30 May 2007 12:00:29 -0400
To:
gmx-users@gromacs.org

To:
gmx-users@gromacs.org



I'm not a QM expert myself (Gerrit, comments?),  but I'm pretty sure  
the main reason is that you cannot either mutate atom types or  
decouple interactions gradually in the QM part of the system. Once  
this is solved for a pure QM system it should be straightforward to  
implement the QM/MM interface of it.


One of the main things we plan to do with the free energy code (once I 
can confirm I'm doing things right) is to modify the charge of the 
quantum system for the lambda values, so atom types don't need to be 
modified for this I believe, although I see how that could complicate 
other types of free energy calculations.  As for decoupling 
interactions I don't know what impact that has for changing of charge.


For now, are there any major complications if all we want to do is 
modify the charge from state A to state B (assuming the interacti

Re:[gmx-users] GAMESS-US for Hybrid QM/MM ( gmx-users Digest, Vol 39, Issue 71 )

[Gerrit Groenhof]

Hi All

   Is there any way to use gamess-us for Hybrid QM/MM calculation with Gromacs instead of using CPMD, GAMESS-uk or gaussion? 

  
Not yet, but feel free to write the interface code. I can help you link 
it all up once an interface code exists. You can either start from 
mdlib/qm_gamess.c which is based on calling fortran routines from a 
precompiled gamess library, or from qm_gaussian,  that uses system calls 
to a gamess-us binary after dumping an input file. The routines 
write_gaussian_input, read_gaussian_output and call_gaussian can serve 
as a base from handling the io and performing the system calls .


With best regards,

Gerrit


Thanks

Dhiraj

  


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[gmx-users] Re: gmx-users Digest, Vol 41, Issue 5: interaction lists in idef.h ([EMAIL PROTECTED])

[Gerrit Groenhof]

   8. interaction lists in idef.h ([EMAIL PROTECTED])

  


Dear Will,

Have a look at 
http://www.mpibpc.mpg.de/groups/grubmueller/start/people/ggroenh/gromacs_I.pdf


In idef there is the ilist array, with an element for each of the F_NRE 
interaction types.


THis list is an 1D array of 1D arrays. Depending on how many atoms are 
involved in a specific interaction (say n), these arrays are multiples 
of n+1, where the first element is an index into an iparams and ifunc 
array. The next elements are the actual atomnumbers in the simulations 
involved in this interactions. The ifunc contains the function, the 
iparams the parameter for that functions.


So if you want to have all the angles: loop though the ilist[F_ANGLE] in 
steps of 4 (see sheet 6) to get all the atoms triples and their 
interaction function (the same for all) and parameters (differnet for 
different atoms combinations).


Hope this will help you a bit further,

Gerrit
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[gmx-users] Re: gmx-users Digest, Vol 41, Issue 10: How to run ED with position restrain along first principle, component (Anirban Ghosh)

[Gerrit Groenhof]

   4. How to run ED with position restrain along first  principle
  component (Anirban Ghosh)
  


You can either keep it fixed with the -linfix option of mk_edi. The 
other option is to use the flooding  code, with a harmonic restraint on 
the eigenvector. Check the paper

Flooding in gromacs by Lange, Schaefer and Grubmueller JCC (2006).

Gerrit
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[gmx-users] Re: mopac gcc g77 and x86_64

[Gerrit Groenhof]

f the
first 3 ps.
A:
 0 136.923 81.5686 218.491   0
 1 136.149 87.5994 223.748   0
 2 136.607 90.9957 227.603   0
B:
 0 129.967 85.1524 215.119   0
 1 140.375  86.953 227.328   0
 2 138.37 90.9806  229.35   0
A+B:
 0 264.215 169.394 433.608   0
 1 274.129 176.945 451.074   0
 2 276.924 180.027 456.951   0

Look forward to your explanation.


Hi Tang,

I think this is actually a roundoff problem. It looks like your  
proteins
make no contact at all. Did you use the -pbc flag (it may be default  
though)




Thank you,

Tang Jiaowei

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End of gmx-users Digest, Vol 42, Issue 102
**


--
Gerrit Groenhof
MPI for Biophysical Chemistry
Am Fassberg 11
D-37077 Goettingen
Germany

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[gmx-users] Re: gmx-users Digest, Vol 43, Issue 49

[Gerrit Groenhof]

What you want to do, a dynamic updating of the QM atoms is not 
implemented yet.
The difficulty with such scheme is energy conservation and force 
conservation when translocating an atom from the MM into the QM region 
and vice versa.
This is a difficult problem. However, there soluitons, see for instance 
Heyden, Lin and Truhlar (J. Phys. Chem. B 2007, 111, 2231-2241).
Therefore, if such a dynamic partitioning is essential for your 
research, you could implement their ideas into gromacs. 


Gerrit




Message: 1
Date: Mon, 12 Nov 2007 15:10:08 -0500
From: "Tandia, Adama" <[EMAIL PROTECTED]>
Subject: [gmx-users] QMMM for element with "unknown" forcefield
To: gmx-users@gromacs.org
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset=US-ASCII

Dear GMX users,

I'm not very familiar with the QMMM implementation in Gromacs, but I
have two questions. 


1- I would like to run a MD simulation for glass materials that
contain B and Sb based oxides. Both elements are known to be multivalent
in the compositions that I'm interested. Is it possible to setup a QMMM
that assigns a sphere where QMMM is performed with a fixed radius around
Sb and B, and have the spheres to move with the assigned atoms during
the simulation? This would be a sort of Learn-On-The-Fly method.

2- Has anyone successfully compiled Gromacs 3.3.2 with QMMM set
to work with Gaussian or CPMD? If yes, can I request the details of the
compilation procedure?

Best wishes,

Adama

 
==

Adama Tandia
Modeling & Simulation
Corning INC
USA
 
Tel:  607 248 1036

Fax: 607 974 3405
www.corning.com

  


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Re: [gmx-users] simulation at particular pH

[Gerrit Groenhof]

Bad idea. Adding just one proton (1/Navogadro moles ~ 1.6 * 10^-24)to a 
box of say 500 nm^3 (5 10^-22 liter), continaining roughly 1 waters 
would give a pH of 2.5  (-log[1.6/5*10^-2), which is the maximum pH you 
can reach for such standard box. If you want to go higher, say to pH=7, 
your box needs to be at least 1.6 * 10^-17 liter, or 1.6 * 10^7 nm^3. 
THis is too big for simulation.


Therefore adding H+ or H3O+ is not really an option. Instead you should 
choose the protonation states of the titrating sites in the system such 
that they correspond to the pH your are interested in. Equilibrium 
exchange of protons between aminoacid sidechains is probably happening 
on a timescale much longer than a typical simulation length.


Gerrit


On Aug 8, 2006, at 9:16 PM, Arthur Roberts wrote:


Hi, Luisa,

I would first calculate the number of protons (H+)
that you would find your water box. Then I would use
the command genion to generate that number of H+'s
that corresponds to the pH.  Then I would use grompp
to find out what the final charge is.  If it is still
negative, I would add NA+.  If it is positive, I would
add CL-.  This should approximate the pH.  Although
there is one problem, ionizable residues.  You will
need to set those manually.  I am not sure, if you can
use the morse potential on specific residues instead
of harmonic potential to make a residue ionizable.  I
hope this helps.

Best wishes,
Art Roberts
University of Washington
Department of Medicinal Chemistry

--- luisa pugliese
<[EMAIL PROTECTED]> wrote:


Hello to everybody,
   I am new to this mailing list and I am writing
because I wonder if anybody knows how can I set up
the pH of the system in gramacs.
Thank you to everybody
Luisa
=
Luisa Pugliese, Ph.D.
[EMAIL PROTECTED]
S.A.F.AN. BIOINFORMATICS
Corso Tazzoli 215/13 -10137 Torino - ITALY
tel +39 011 3026230
fax +39 011 3165080
cell. +39 333 6130644

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Re: [gmx-users] How can I remove water and ion molecules

[Gerrit Groenhof]

make an index file entry with the stuff you want to write in your pdb,  
and use editconf -n to dump only that.



On Sep 25, 2006, at 5:05 PM, Guillem Portella wrote:



man grep

with special attention to -v option

bounus ball: it also works before em and md

Cheers


On Monday 25 September 2006 15:55, jahanshah ashkani wrote:

Hi,
How can I remove water and ion molecules from the pdb file after  
energy

minimization and molecular dynamic simulation? Thank you very much.

Sincerely yours,


Jahanshah Ashkani,
PhD student of Biotechnology & Genetics,
University of the Western Cape,
Biotechnology Department,
Private Bag X17,
7735 Bellville,
Cape Town,
South Africa
[EMAIL PROTECTED]

-
Do you Yahoo!?
 Everyone is raving about the  all-new Yahoo! Mail.


--  
***

 Guillem Portella
 Computational biomolecular dynamics group at the
 Max Planck Institute for Biophysical Chemistry
 Am Fassberg 11
 D-37077 Goettingen -- Germany --
 phone: ++49-551-2012309
 fax: ++49-551-2012302
 Email: [EMAIL PROTECTED]
  
webpage:http://www.mpibpc.mpg.de/groups/grubmueller/start/people/ 
gportel/index.php

***
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Re: [gmx-users] QMMM interface

[Gerrit Groenhof]

It does not exist, but since gmx is open source, I suggest you give it 
a try. I suppose the input/output is similar to gamess-uk? In that 
case, have a look at  mdlib/qmmm.c and gamess.c. Contact me off list at 
ggroenh<>gwdg.de if you need more help.


Gerrit


On Sep 28, 2006, at 3:01 PM, [EMAIL PROTECTED] wrote:



Dear Gromacs users,

I have been using Pcgamess for QM calculations, which is a very fast 
(and free) program, and has some QMMM capabilities(but a size limit of 
about 1000 atoms ). I just found out that Gromacs now has QMMM 
capabilities with CPMD, Gaussian and Gamess(UK). Does any one know 
whether a Gromacs-PcGamess QMMM interface is planned? It would be 
great for those of us with small research budgets, and who cannot 
afford the comercial QM codes.


Pedro


Enviado por https://webmail.ufp.pt


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Re: [gmx-users] qm_mopac.c problems in building of 3.3.1

[Gerrit Groenhof]

Hi Jake,

Did you add to the mopac library the gmxmop.o, and dcart.o 
(http://rugmd4.chem.rug.nl/~groenhof/qmmm.html#code) before linking to 
gromacs?


The functions domldt and domop are in gmxmop.

Gerrit


On Oct 6, 2006, at 8:41 PM, Jake Michaelson wrote:



Hi all,

I'm trying to build a qmmm-enabled version of gromacs 3.31 with MOPAC7.
My specs:

Intel Core 2 Duo
Ubuntu 6.06 with kernel 2.6.18-ck1 (x86-64)
compiling with Intel MKL 8.1.1, icc v 9.1, ifort v 9.1
MOPAC7 v 1.10

MOPAC compiles nicely with the above, but when I try to build gromacs
with:

export LIBS="-lmkl -lguide -lpthread -lmkl_lapack -lmopac7 -lg2c"

./configure --prefix=/usr --with-fft=mkl --with-external-blas
--with-external-lapack --with-qmmm-mopac --with-x

Make eventually dies with (snippet):

../mdlib/.libs/libmd.a(qm_mopac.o): In function `/bin/sh ../../libtool
--tag=CC --mode=link /opt/intel/cce/9.1.043/bin/icc  -openmp -xT
-L/usr/atlas/lib -L/opt/intel/cce/9.1.043/lib
-L/opt/intel/fce/9.1.037/lib -L/usr/lib64  -o protonate hackblock.o
ter_db.o h_db.o genhydro.o pgutil.o resall.o add_par.o topexcl.o
toputil.o topdirs.o protonate.o ../mdlib/libmd.la ../gmxlib/libgmx.la
-L/usr/X11R6/lib -lnsl -lmkl -lmkl -lguide -lpthread -lmkl_lapack
-lmopac7 -lg2c  -lSM -lICE -lX11
call_mopac':qm_mopac.c:(.text+0x135): undefined reference to `domop_'
../mdlib/.libs/libmd.a(qm_mopac.o): In function
`call_mopac_SH':qm_mopac.c:(.text+0x38f): undefined reference to
`domop_'
../mdlib/.libs/libmd.a(qm_mopac.o): In function
`init_mopac':qm_mopac.c:(.text+0x541): undefined reference to `domldt_'
make[3]: *** [mdrun] Error 1

...basically undefined references to domop_ and domldt_ in qm_mopac.c.
I'm not sure where these are supposed to be found.  Can anyone give me 
a

hand on this?

For what it's worth I've also tried building both MOPAC7 and gromacs 
with gcc, but I got exactly the same error, which suggests that this 
is not a compiler-specific problem.


Thanks,

Jake


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Re: [gmx-users] QMMM gromacs/CPMD

[Gerrit Groenhof]

(1) For QM/MM, even simple QM solute in a MM solvent, Lennard Jones 
parameters are required to compute the Van der Waals interactions 
between the QM and MM subsystems.
Thus one always needs to give the atoms types for the atoms in the QM 
system.


A simple topology file will do, containing only the [ atoms ] section, 
with the atoms of your QM solute. To avoid problems when the QM 
subsystem moves over the boundary during a simulation, it is advisable 
to define the bonds between the atoms as well, using bondtype 5 in the 
[ bonds ] section. This bondtype does not have a function nor 
parameters, but allows gromacs to make the molecule whole again before 
every QM computation.


(2) You can try  prdrg.

(3) QM/MM Electrostatics inside CPMD are handled different from the 
electrostatics in gromacs. The precise details I do not know. Maybe 
Pradip Kumar Biswas can add something to this?


(4). Setting the cut-off to 0 means infinite cut-off, and works in 
vacuum only. For pbc, use a finite cut-off and PME or ReactionField. I 
suppose the example you are talking about concerns a minimization of 
some QM/MM system in vacuo.


Best,

Gerrit


On Nov 3, 2006, at 4:35 PM, Loison Claire wrote:


Dear gmx-users,

I would like to test the gromacs/CPMD combinaison for  QMMM 
calculations.
For the system I am interested in, the configuration is "relatively 
simple", the model contains
a single quantum solute molecule surrounded by classical solvent 
molecules (water, let say).
So no broken bonds, and no dummy atoms. But it's complicated because 
it's a liquid phase.


So i want to build the topology, including  for example the 
"solute.itp" file.
What puzzles me, is that i should give some information about a 
classical force field
describing the atoms in my quantum solute... But i cannot set in 
advance agood classical force field for it:

If I had, i would not bother  about QMMM.

So I have several questions about the gromacs/CPMD:
(1)  does gromacs use at the force-field parameters concerning the 
quantum atoms  ?

When and for what ? How critical are those parameters ?
(2) i think about  building a quick and dirty approximate classical 
force field for my solute molecule, in order to
create classically a starting point before doing the QMMM. But of 
course as my force-field is probably bad,
the system may explode as soon as i change the model. So do you have 
some advise how to construct my first system ?

(3)  an other question which is more CPMD related : i am now testing
the  influence of size of the quantum bounding box
and the poisson solver on the electronic structure of my solute.
As i understood, this SYMMETRY 0 is in order to avoid
seeing the electrostatic periodic  images which
are instrinsically present in plane-wave calculation.
In vacuum it's exactly what i want. But my QMMM system  is a liquid, i 
want to have periodic

boundary conditions for my MM box (the gromacs'one, not the CPMD one).
What does the QM system feel if i  take the ususal pbc of gromacs 
input ?  Does it see its

periodic  images (I mean with the periodicity of  the MM box ) ?
Do i have to take care that the QM system does not cross the boundary 
of the MM box ?
(4) in the examples from the Gogonea's group ( 
http://comppsi.csuohio.edu/groups/qmmm.html,
which i had difficulties to run, by the way), the gromacs cutoff  for 
the electrostatic interaction is set to 0.

Is that compulsory ?

Thanks for any suggestions and for your understanding about confused 
questions..


Claire Loison

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Re: [gmx-users] does gromos force field can explain pi-pi interaction

[Gerrit Groenhof (RUG)]

The most recent paper I read on this is by Piacenza and Grimme (J. AM. 
CHEM. SOC. 2005, 127, 14841-14848 ).
They use a very efficient DFT based approach with an empirical 
correction to compute accurate stacking energies. At least so they say. 
Unfortunately their method DFT-D is not yet available in any of the 
quantum chemistry programs that can be linked to gromacs.


Gerrit

Diane Fournier wrote:


I have read a lot on this subject since I wanted to prove one such interaction 
myself (between inhibitor and enzyme).

Generally, authors who talk of such interaction never give proof using 
simulation, but use a simple geometric criteria (benzene rings are superposed 
in T-shape or face-to-face staggered configuration at a given distance) to 
describe them in crystal structures.

For modeling, there are a few papers (beginning 1990s, not quite recent) which 
used a point charge model to model pi-pi stacking (Hunter-Saunders model). In 
this model, charges are distributed onto the hydrogens and in the middle of the 
benzene ring (with a dummy atom) and their results (geometry optimization) 
showed some similarity to experimental results seen in crystals. I can give you 
the references if you like.

However, pi-pi interactions have some polarization component, and so they have 
been best modeled with quantum mechanics; this would involve doing a QMMM 
simulation. I have not seen yet a paper talking about QMMM simulation of pi-pi 
stacking (if somebody has seen one please give me the reference)

I have also heard of polarizable force fields, but I don't know if they can 
model pi-stacking properly.

If somebody has heard of a proven method of modeling pi-stacking, energy- and 
geometry-wise, I would also be very interested in it.

Diane

  



-Original Message-
From: [EMAIL PROTECTED] on behalf of Wei Fu
Sent: Wed 7/26/2006 11:44 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] does gromos force field can explain pi-pi interaction

Dear gmx users,

   My simulation shows that the aromatic ring of ligand forms stacking
pi-pi interaction with the side chain of Phe of receptor during MD
simulation.
One reviewer of my manuscript questions that such pi-pi interaction can
not accurately accounted for by the employed force field.  


I do not know how to answer this question, any idea is highly appreciated!

Linda


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Re: [gmx-users] langevin dynamics

[Gerrit Groenhof (RUG)]

I think you do not use the bd_fric in combination with sd, but with bd, 
the friction is set by the tau_t instead. Did you als use different 
parameters for that?


For bd, you would use the friction bd_fric to set the ld friction, but 
not for sd, but I could be wrong here...


Gerrit

syma wrote:


Hi,

I have been having a few problems running Langevin dynamics and was
wondering if anyone can help.

I have run both atomistic and coarse grain LD simulations in gromacs 3.1 3.2
and 3.3. The puzzling thing is that changing the value of the frictional
constant makes no difference to the simulations. Ie RMSD values are EXACTLY
the same when simulations are run with different frictional constants.

I have used gmxdump to analyse the tpr files- the correct values for the
frictional term does seem to be picked up. The mdp file I have been using is
attached. If anyone can see anything obviously wrong with the file I would
appreciate your advice.

Best wishes,

-Syma 


***

Dr Syma Khalid  
Department of Biochemistry,   
University of Oxford   
South Parks Road,

Oxford
OX1 3QU
U.K.



***


 




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Re: [gmx-users] PME usage in 3.3 & g_energy: doubt ?

[Gerrit Groenhof (RUG)]

First, with rlist = rvdw, you will not get long range Lennard Jones 
interactions. In fact I would recommend using a larger vdw cut-off, as 
0.9 is very short. Are you sure you are using the same mdp file?


About the LR coulomb, it will only appear if you have rlist < rcoulomb. 
In that case the sphere between rlist and rcoulomb is frozen for the 
direct electrostatic interaction calculation during PME between two 
nlist updates (set by nlist = X).


Gerrit

Luca Mollica wrote:


Hi,

having started to use GMX 3.3 since few months, I have a doubt about 
using PME treatement for electrostatics and extracting energies from 
the corresponding .edr file.


After simulation, trying to use g_energy -f energy.edr -o Energy.xvg, 
I get the following groups:


[...]
Mu-YMu-ZCoul-SR:Protein-Protein
LJ-SR:Protein-Protein   Coul-14:Protein-Protein LJ-14:Protein-Protein
Coul-SR:Protein-SOL LJ-SR:Protein-SOL   Coul-14:Protein-SOL
LJ-14:Protein-SOL   Coul-SR:Protein-Cl  LJ-SR:Protein-Cl
Coul-14:Protein-Cl  LJ-14:Protein-ClCoul-SR:SOL-SOL
LJ-SR:SOL-SOL   Coul-14:SOL-SOL LJ-14:SOL-SOL
Coul-SR:SOL-Cl  LJ-SR:SOL-ClCoul-14:SOL-Cl

[...]

I have notice a difference with respect to 3.2 version of GMX, that is 
the absence of LR terms for both LJ and Coulombic terms: 3.2 provides 
a LR term for PME calculations, 3.3 does not provide it.
Now, what about the missing terms ? Considering the theory that stays 
behind the Ewald sums, the SR term should include only the real part, 
but I cannot understand quite well what I have to do with the 
'missing' reciprocal + dipolar + self LR term 


Please consider that I have used the following terms for energy 
calculations:


pbc =  xyz
ns_type =  grid
rlist   =  0.9
rcoulomb=  0.9
fourierspacing  =  0.12
pme_order   =  4
rvdw=  0.9
coulombtype =  PME
ewald_rtol  =  1e-5

which corresponds to pretty standard PME parameters  and also, 
testing Cut Off treatement of electrostatics, I get back the LR and SR 
term.


ThanX to you all




Luca




:: 



Luca Mollica
Dulbecco Telethon Institute
c/o DIBIT - S. Raffaele Scientific Institute
Biomolecular NMR Laboratory, 1B4
Via Olgettina 58
20132 Milano Italy

Tel: 00390226433497
Fax: 00390226434153


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which can be made in a narrow field.

(Niels Bohr)




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Re: [gmx-users] what is "MPI process rank 0 (n0, p18041) caught a SIGSEGV"

[Gerrit Groenhof (RUG)]

Recompile the mopac library with larger arrays. You can set these in the 
SIZES file in the mopac sourcedir

(MAXORB).

Do not forget to recompile also mdrun afterwards,as the library (.a) 
will be statically linked.


Gerrit

Mahnam wrote:



In God We Trust
Hello GMX users
I want to do QM/MM by Gromacs and mopac7.I installed Gromacs and 
mopac7.I am using ffoplsaa. grompp make tpr ,but when I run mdrun it 
says:

Back Off! I just backed up a.log to ./#a.log.5#
Reading file a4.tpr, VERSION 3.3 (single precision)
QM/MM calculation requested.
Layer 0
nr of QM atoms 147
QMlevel: PM3/STO-3G
 
   MAXIMUM NUMBER OF ATOMIC ORBITALS EXCEEDED

   MAXIMUM ALLOWED = 200
keywords are: PRECISE GEO-OK CHARGE=0 GRAD MMOK ANALYT PM3

Back Off! I just backed up a.edr to ./#a.edr.5#
Steepest Descents:
   Tolerance (Fmax)   =  1.0e+02
   Number of steps= 1000
 counting the number of NH-C=O groups
*MPI process rank 0 (n0, p18041) caught a SIGSEGV*.

and here is the end of my md.log file
Initializing LINear Constraint Solver
  number of constraints is 6
  average number of constraints coupled to one constraint is 0.0
Steepest Descents:
   Tolerance (Fmax)   =  1.0e+02
   Number of steps= 1000
   Rel. Constraint Deviation:  Maxbetween atoms RMS
   Before LINCS 0.098311   1707   1710   0.093123
After LINCS 0.03   1684   1687   0.01
Going to use C-settle (1267 waters)
wo = 0.33, wh =0.33, wohh = 3, rc = 0.08165, ra = 0.0384897
rb = 0.0192449, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1
Grid: 9 x 9 x 6 cells
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.
 
I do not have any idea why this is happening?.May I ask you what does 
it means?

Any help will be greatly appreciated
 
Karim Mahnam

Institute of  Biochemistry  and  Biophysics (IBB)
Tehran University
P.O.box 13145-1384
Tehran
Iran
http://www.ibb.ut.ac.ir/



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Re: [gmx-users] Vacuum simulation problem

[Gerrit Groenhof (RUG)]

Do not use Pressure coupling in vacuo. ALso you seem to be running with 
periodic boundary conditions. Switch that off as well and use ns_type = 
simple, and finally use infinite cut-offs when simulating in vacuo. qa 
cut-off of 0.9 is way too short. If you think the lack of water causes 
the conformatational changes and you don't want that, you can try 
putting position restraints on backboneatoms of solvent exposed residues.


Gerrit



[EMAIL PROTECTED] wrote:


Dear all,
I am simulating a protein containing 2 domains which are linked together 
by a loop of around 10 residues. When I am simulating the same in vacuum, 
after approx 1ns, the rmsd has increased from 5 angstroms to 25 angstroms 
with in 10 time steps. You can surely imagine how drastic the structural 
changes are happening. 
What exactly might be happening there, why the protein is behaving like 
that. I am pasting the mdp file below. 
;   User spoel (236)

;   Wed Nov  3 17:12:44 1993
;   Input file
;
title   =  Yo
cpp =  /lib/cpp
constraints =  all-bonds
;define  =  -DPOSRES
integrator  =  md
dt  =  0.002; ps !
nsteps  =  1000 ; total 1 ps.
nstcomm =  1
nstxout =  500
nstvout =  500
nstfout =  500
nstlog  =  500
nstenergy   =  500
nstlist =  10
ns_type =  grid
rlist   =  0.9
rcoulomb=  0.9
rvdw=  0.9
; Berendsen temperature coupling is on in two groups
Tcoupl  =  berendsen
tc-grps =  Protein
tau_t   =  0.1
ref_t   =  300
; Energy monitoring
energygrps  =  Protein
; Isotropic pressure coupling is now on
Pcoupl  =  berendsen
Pcoupltype  = isotropic
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is off at 300 K.
gen_vel =  no
gen_temp=  300.0
gen_seed=  173529


kindly guide me in this issue.
regards
Anwar

--
Mohd Anwaruddin
Project Assistant
C/o DR.H.A.Nagarajaram
Lab of Computational Biology and Bioinformatics
Center for DNA Fingerprinting and Diagnostics(CDFD)
Nacharam
Hyderabad-500 076
INDIA.
Tel: +91-8413-235467,68,69,70 ext 2019
[EMAIL PROTECTED]
---



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Re: [gmx-users] vacuum simulation problem

[Gerrit Groenhof (RUG)]

In addition to Erik and my suggestions, you should also remove the 
overall rotation: comm_mode=linear.


[EMAIL PROTECTED] wrote:


Dear all,
I am simulating a protein containing 2 domains which are linked together 
by a loop of around 10 residues. When I am simulating the same in vacuum, 
after approx 1ns, the rmsd has increased from 5 angstroms to 25 angstroms 
with in 10 time steps. You can surely imagine how drastic the structural 
changes are happening. And also during the simulation after 500ps the protein 
started to rotate and later at approx 2ns the protein stopped rotation. 
What exactly might be happening there, why the protein is behaving like 
that. I am pasting the mdp file below. 
;   User spoel (236)

;   Wed Nov  3 17:12:44 1993
;   Input file
;
title   =  Yo
cpp =  /lib/cpp
constraints =  all-bonds
;define  =  -DPOSRES
integrator  =  md
dt  =  0.002; ps !
nsteps  =  1000 ; total 1 ps.
nstcomm =  1
nstxout =  500
nstvout =  500
nstfout =  500
nstlog  =  500
nstenergy   =  500
nstlist =  10
ns_type =  grid
rlist   =  0.9
rcoulomb=  0.9
rvdw=  0.9
; Berendsen temperature coupling is on in two groups
Tcoupl  =  berendsen
tc-grps =  Protein
tau_t   =  0.1
ref_t   =  300
; Energy monitoring
energygrps  =  Protein
; Isotropic pressure coupling is now on
Pcoupl  =  berendsen
Pcoupltype  = isotropic
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is off at 300 K.
gen_vel =  no
gen_temp=  300.0
gen_seed=  173529


kindly guide me in this issue.
regards
Anwar

--
Mohd Anwaruddin
Project Assistant
C/o DR.H.A.Nagarajaram
Lab of Computational Biology and Bioinformatics
Center for DNA Fingerprinting and Diagnostics(CDFD)
Nacharam
Hyderabad-500 076
INDIA.
Tel: +91-8413-235467,68,69,70 ext 2019
[EMAIL PROTECTED]
---



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