Re:Re: [gmx-users] remd with different potential at different temperature

[杜波]

dear teacher,
if i want to do remd  with different tabulated potentials.
how can i use the mdrun's   -table (-table table.xvg -tableb table.xvg )?
if it can also use like that,there is another question:
and how can i rename the tables name ( table_CR1_CR1: i rename
them table_CR1_CR10,table_CR1_CR11,table_CR1_CR12...,
i test this is wrong!!!
 )
thanks
> regards,
> PHD, Bo Du
> Department of Polymer Science and Engineering,
> School of Chemical Engineering and technology,
> Tianjin University, Weijin Road 92, Nankai District 300072,
> Tianjin City P. R. China
> Tel/Fax: +86-22-27404303
> E-mail: 2008d...@gmail.com 





Message: 1
Date: Tue, 08 Nov 2011 17:55:49 +1100
From: Mark Abraham 
Subject: Re: [gmx-users] remd with different potential at different
   temperature
To: Discussion list for GROMACS users 
Message-ID: <4eb8d275.2010...@anu.edu.au>
Content-Type: text/plain; charset="iso-8859-1"

On 8/11/2011 5:43 PM, ?? wrote:
> dear teacher,
> how can i do remd with different non-bond potential at different
> temperature ?
> easy to say ,can i use different *.top at diferent temperature.

Probably. Try a simple case and see. The REMD implementation checks only
certain critical quantities are constant over the generalized ensemble.
See the lines that begin "Multi-checking" in an REMD .log file. You can
probably even use different tabulated potentials for each replica.

Mark

>
> if not ,can you give me some suggestions to rewrite the gromacs codes.
> thanks!!
>
> regards,
> PHD, Bo Du
> Department of Polymer Science and Engineering,
> School of Chemical Engineering and technology,
> Tianjin University, Weijin Road 92, Nankai District 300072,
> Tianjin City P. R. China
> Tel/Fax: +86-22-27404303
> E-mail: 2008d...@gmail.com 
>
>
>
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Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)

[Micha Ben Achim Kunze]

I am not sure I understand exactly what you mean but this is all covered 
in Gerrit's QM/MM tutorials, I'd recommend you go through those. In the 
ORCA files there is no need to do anything with LAs, GMX will hand a 
file with the QMsubsystem to ORCA which includes the LA as hydrogens in 
your case I guess.


Cheers,
Micha
On 08/11/11 07:07, xi zhao wrote:

Thank you for your suggest, my gromacs reinstalled: ./configure --
--without-qmmm-gaussian  --without-qmmm-orca 
when mpirun -np 1 mdrun_p -v -s pyp_qm.tpr,

Back Off! I just backed up md.log to ./#md.log.1#
Getting Loaded...
Reading file pyp_qm.tpr, VERSION 4.5.3 (double precision)
Loaded with Money
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 22
QMlevel: RHF/3-21G
/home/user/orca_x86_64_exe_r2131/home/user/orca_x86_64_exe_r2131...
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.1#
starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water'
500 steps,  0.5 ps.
Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp >> pyp_qm.out'
   Unless this is specifically allowed this means that the basis set 
is not

   available for this element - Aborting the run
---
Program mdrun_p, VERSION 4.5.3
Source code file: qm_orca.c, line: 409
Fatal error:
Call to '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp >> 
pyp_qm.out' failed

..
but a question raised:  how to deal with LA in the QMatoms in orca 
inputfile? using DA ( dummy atom in the ORCA) repaces LA in the 
QMatoms in the gromacs ?

please give me a suggestion!
Thank you!
4 



--- *11年11月7日，周一, Micha Ben Achim Kunze 
//* 写道：



发件人: Micha Ben Achim Kunze 
主题: Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)
收件人: gmx-users@gromacs.org
日期: 2011年11月7日,周一,下午10:50

From the output it looks like you forgot the
--without-qmmm-gaussian flag while compiling.

Micha
On 07/11/11 14:42, xi zhao wrote:

When remove these lines, the errros still :Fatal error:
Invalid QMMM input: 1 groups 0 basissets and 0 methods;
when put something there, (
QMmethod =rhf;QMbasis =sto-3g),

grompp_a -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o
pyp_qm.tpr -maxwarn 10
mpirun -np 8 mdrun_a -v -s pyp_qm.tpr
..
Back Off! I just backed up md.log to ./#md.log.7#
Getting Loaded...
Reading file pyp_qm.tpr, VERSION 4.5.3 (double precision)
Loaded with Money
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
there we go!
QM/MM calculation requested.
QM/MM calculation requested.
there we go!
there we go!
there we go!
there we go!
there we go!
there we go!
there we go!
Layer 0
nr of QM atoms 22
QMlevel: RHF/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

-
One of the processes started by mpirun has exited with a nonzero exit
code.  This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.
PID 11786 failed on node n0 (127.0.0.1) due to signal 11.
how to deal with?
4


--- *11年11月7日，周一, Gerrit Groenhof /
/*
写道：


发件人: Gerrit Groenhof 

主题: [gmx-users] Re 1. orca and qm/mm (xi zhao)
收件人: gmx-users@gromacs.org

日期: 2011年11月7日,周一,下午9:23

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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Re: [gmx-users] A question about deuteriu order parameters graph

[Javier Cerezo]

Hi Alex

Deuterium order parameter is a property related to the relative 
orientation of molecular axis taking the bilayer normal as reference. 
How to use them to extract useful structural information is a matter of 
how you interpret the values regarding their definition (see e.g. 
Egberts and Berendsen [J. Chem. Phys.(1988), vol 89, 3718] or Heller et 
al [J. Phys. Chem. (1993), vol 97, 8343]). In general, by comparing 
order parameters of different systems you can have some hints about the 
phase or ordering of your different systems and how it may change (for 
example at different temperature or after insertion of a membrane protein).


Morover, the usefulness of this paramenter mainly comes from the fact 
that they are readily available from simulations and thus can be used to 
validate your methodology. Concretely, experimental information about 
the deuterium order parameter (Scd, the one you reported) is spread over 
the scientific literature about membranes (see e.g. the series of papers 
from the J.F Nagle's group) and it is the deuterium order parameter 
commonly reported in MD simulations. For the case of DPPC you can take 
for example the ones from Petrache et al [Biophys. J (2000), vol 79, 
3172] and Douliez et al [Biophys. J. (1995), vol 68, 1727]. Take into 
account that GROMACS g_order tool just numerate your atoms in the order 
the order parameters are calculated: the first Scd comes from the second 
atom in the index, per the calculation procedure, so is the CH2 close to 
the carbonyl (normally numbered as 2 in the chain).


In your case, if you compare your graphs with the experimental ones 
(pure bilayers), they are significantly different, which may arise from 
the fact of the protein insertion (I doubt it, however) or indicate an 
incorrect MD calculation (bad parameters, not well converged...) or 
incorrect Scd calculation. Please, post your MD details (FF, mdp 
file...) and how you calculated the Scd to continue the discussion. Did 
you calculate the Scd on the pure bilayer?


Javier


El 08/11/11 06:41, Alex escribió:

Dear All,

I run a MD simulation on a membrane protein using DPPC and I performed a
deuterium order parameters on the trajectory.
As I'm a newbie, could you kindly help me to give an interpretation of these
graphs?

You can open them at:
sn1
http://www.freeimagehosting.net/137c9

sn2
http://www.freeimagehosting.net/6e321


Thanks in advance



--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tlf.(+34)868887434

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Re: [gmx-users] Re: PBC - Protein - ligand

[Steven Neumann]

On Mon, Nov 7, 2011 at 9:47 PM, Justin A. Lemkul  wrote:

>
>
> Steven Neumann wrote:
>
>> Hi Tsjerk,
>>
>> Thank you. Unfortunately my ligand is not with protein. I put my ligand
>> around my protein (in water) running separate simulations to see where can
>> it bind. It is close to protein but not within. Any other suggestion?
>> I used also pbc -res so I observe my ligand close to protein but
>> sometimes still changing its position rapidly... No clue for now how to
>> solve it...
>>
>>
> I have no idea why the proposed protocol isn't working, but I know that
> one should be able to do something very simple, along the lines of the
> following, for this to work:
>
> 1. trjconv -s md.tpr -f md.xtc -o pbc_fix.xtc -pbc mol
> 2. trjconv -s md.tpr -f pbc_fix.xtc -o center.xtc -center (center on the
> protein)
> 3. trjconv -s md.tpr -f center.xtc -o fit.xtc -fit rot+trans (choose
> protein for fitting)
>
> -Justin
>
>
Thank you Justin. From this workflow my ligand is binding the protein most
of the frames but sometimes it rapidly jumps to different part of the box
and come back again. Then remains with protein and situation is repeated:
in one frame it changes its position and come back to protein remaining.
:( no clue...



> Steven
>>
>>
>> On Monday, November 7, 2011, Tsjerk Wassenaar > tsje...@gmail.com>> wrote:
>>  > Hi Steven,
>>  >
>>  > Step 2: Cluster your molecules.
>>  > This is where you have to forge a reference frame that you can use to
>>  > remove jumps from your trajectory. If the ligand is not with the
>>  > protein at the start, you'll have to shift it so that it is. Maybe
>>  > -pbc cluster is your friend there. I do assume that the ligand is
>>  > really with the protein and not in the solvent...
>>  >
>>  > Cheers,
>>  >
>>  > Tsjerk
>>  >
>>  > On Mon, Nov 7, 2011 at 5:17 PM, Steven Neumann 
>> > s.neuman...@gmail.com>**> wrote:
>>
>>  >>
>>  >>
>>  >> On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>  >>>
>>  >>>
>>  >>> Steven Neumann wrote:
>>  
>>   Dear Gmx Users,
>>    I know that this problem has been discussed may times but I cannot
>> find
>>   the solution to get rid of pbc in my system: protein and ligand. I
>> followed
>>   the workflow:
>>  
>>   1.  First make your molecules whole if you want them whole
>>  
>>   trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc
>>  
>>   2.  Cluster your molecules/particles if you want them clustered
>>  
>>   3.  Extract the first frame from the trajectory as reference for
>>   removing jumps if you want to remove jumps.
>>  
>>   trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb
>>  
>>   4.  Remove jumps if you want to have them removed using the
>> first
>>   frame
>>  
>>   trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o
>> mdwholeNOjump.xtc
>>  
>>   5.  Center your system using some criterion. Doing so shifts the
>>   system, so don't use |trjconv -|pbc| nojump| after this step.
>>  
>>   trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc
>>  
>>   6.  Put everything in some box.
>>  
>>   trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o
>>   mdwholeNOjumpCENTERbox.xtc
>>  
>>   7.  Fit if desired and don't use any PBC related option
>> afterwards.
>>  
>>   trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit
>> rot+trans -o
>>   mdfinal.xtc
>>  
>>  
>>   I used SYSTEM everywhere as output orinput. However, my ligand is
>> still
>>   jumping like a fly around the stable protein. Do you have any
>> suggestions?
>>  
>>  
>>  >>>
>>  >>> Center on either the protein, the ligand, or some custom index group
>> of
>>  >>> residues surrounding the ligand.  Centering on the whole system
>> usually
>>  >>> doesn't do anything useful.
>>  >>>
>>  >>> -Justin
>>  >>>
>>  >>
>>  >> Thank you guys but...
>>  >>
>>  >> I am trying and it does not work... my ligand is jumping like an idiot
>>  >> outside the box changing its position even two dimensions of box in
>> one
>>  >> frame. I removed -ur compact from the first line and I tried
>> centering on
>>  >> ligand or protein (centering group: LIG or Protein, output: SYSTEM).
>> No
>>  >> results...
>>  >> My ligand at the begining of the simualtion is not within the protein.
>>  >> Please, help : I tried this workflow with many ligands and same
>> protein
>>  >> - it worked! Now it does not...
>>  >> Here is my workflow:
>>  >>
>>  >>
>>  >> 1.  First make your molecules whole if you want them whole.
>>  >>
>>  >> trjconv -f md.trr -s md.tpr -pbc whole -o mdwhole.xtc
>>  >>
>>  >> 2.  Cluster your molecules/particles if you want them clustered
>>  >>
>>  >> 3.  Extract the first frame from the trajectory as reference for
>>  >> removing jumps if you want to remove jumps.
>>  >>
>>  >> trjconv -f mdwho

Re: [gmx-users] Re: PBC - Protein - ligand

[Steven Neumann]

Thank you Justin, Mark and Tsjerk.

I used the following workflow


trjconv -s md.tpr -f md.xtc -o pbc_fix.xtc -pbc mol

trjconv -s md.tpr -f pbc_fix.xtc -n index.ndx -pbc cluster -o
pbcfixcluster.xtc  (Protein+ligand group)

trjconv -s md.tpr -f pbcfixcluster.xtc -o center.xtc -center (center on the
protein)


trjconv -s md.tpr -f center.xtc -o Cluster1.xtc -fit rot+trans (choose
protein for
fitting)

Trajectory looks very good from the time when ligand stacked to the
protein (90% of trajectory) but at the begining of the trajectory (when it
is away from protein) it still jumps. I think that is the best solution I
have found. If you know how to fix begining please let me know.

Steven



On Tue, Nov 8, 2011 at 8:53 AM, Steven Neumann wrote:

>
>
>  On Mon, Nov 7, 2011 at 9:47 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> Steven Neumann wrote:
>>
>>> Hi Tsjerk,
>>>
>>> Thank you. Unfortunately my ligand is not with protein. I put my ligand
>>> around my protein (in water) running separate simulations to see where can
>>> it bind. It is close to protein but not within. Any other suggestion?
>>> I used also pbc -res so I observe my ligand close to protein but
>>> sometimes still changing its position rapidly... No clue for now how to
>>> solve it...
>>>
>>>
>> I have no idea why the proposed protocol isn't working, but I know that
>> one should be able to do something very simple, along the lines of the
>> following, for this to work:
>>
>> 1. trjconv -s md.tpr -f md.xtc -o pbc_fix.xtc -pbc mol
>> 2. trjconv -s md.tpr -f pbc_fix.xtc -o center.xtc -center (center on the
>> protein)
>> 3. trjconv -s md.tpr -f center.xtc -o fit.xtc -fit rot+trans (choose
>> protein for fitting)
>>
>> -Justin
>>
>>
> Thank you Justin. From this workflow my ligand is binding the protein most
> of the frames but sometimes it rapidly jumps to different part of the box
> and come back again. Then remains with protein and situation is repeated:
> in one frame it changes its position and come back to protein remaining.
> :( no clue...
>
>
>
>> Steven
>>>
>>>
>>> On Monday, November 7, 2011, Tsjerk Wassenaar >> tsje...@gmail.com>> wrote:
>>>  > Hi Steven,
>>>  >
>>>  > Step 2: Cluster your molecules.
>>>  > This is where you have to forge a reference frame that you can use to
>>>  > remove jumps from your trajectory. If the ligand is not with the
>>>  > protein at the start, you'll have to shift it so that it is. Maybe
>>>  > -pbc cluster is your friend there. I do assume that the ligand is
>>>  > really with the protein and not in the solvent...
>>>  >
>>>  > Cheers,
>>>  >
>>>  > Tsjerk
>>>  >
>>>  > On Mon, Nov 7, 2011 at 5:17 PM, Steven Neumann 
>>> >> s.neuman...@gmail.com>**> wrote:
>>>
>>>  >>
>>>  >>
>>>  >> On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul 
>>> >> jalem...@vt.edu>> wrote:
>>>  >>>
>>>  >>>
>>>  >>> Steven Neumann wrote:
>>>  
>>>   Dear Gmx Users,
>>>    I know that this problem has been discussed may times but I
>>> cannot find
>>>   the solution to get rid of pbc in my system: protein and ligand. I
>>> followed
>>>   the workflow:
>>>  
>>>   1.  First make your molecules whole if you want them whole
>>>  
>>>   trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc
>>>  
>>>   2.  Cluster your molecules/particles if you want them clustered
>>>  
>>>   3.  Extract the first frame from the trajectory as reference
>>> for
>>>   removing jumps if you want to remove jumps.
>>>  
>>>   trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb
>>>  
>>>   4.  Remove jumps if you want to have them removed using the
>>> first
>>>   frame
>>>  
>>>   trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o
>>> mdwholeNOjump.xtc
>>>  
>>>   5.  Center your system using some criterion. Doing so shifts
>>> the
>>>   system, so don't use |trjconv -|pbc| nojump| after this step.
>>>  
>>>   trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc
>>>  
>>>   6.  Put everything in some box.
>>>  
>>>   trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o
>>>   mdwholeNOjumpCENTERbox.xtc
>>>  
>>>   7.  Fit if desired and don't use any PBC related option
>>> afterwards.
>>>  
>>>   trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit
>>> rot+trans -o
>>>   mdfinal.xtc
>>>  
>>>  
>>>   I used SYSTEM everywhere as output orinput. However, my ligand is
>>> still
>>>   jumping like a fly around the stable protein. Do you have any
>>> suggestions?
>>>  
>>>  
>>>  >>>
>>>  >>> Center on either the protein, the ligand, or some custom index
>>> group of
>>>  >>> residues surrounding the ligand.  Centering on the whole system
>>> usually
>>>  >>> doesn't do anything useful.
>>>  >>>
>>>  >>> -Justin
>>>  >>>
>>>  >>
>>>  >> Thank you guys but...
>>>  >>
>>>  >> I am trying and it does not work... my ligand is jumping like

[gmx-users] mdp file problem

[madhumita das]

Hi GROMACS users,

i am in the midst of simulating  a protein in water.  I have modified
a residue  in my  pdb file at position  182,  using amber and then
acpype.py.  But  after running  the energy minimization step,using  em.mdp
file  generated from acpype , following error comes.

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps= 5000
Step=   17, Dmax= 1.5e-06 nm, Epot=  9.89827e+17 Fmax= inf, atom=
2700
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 18 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  9.8982703e+17
Maximum force =inf on atom 2700
Norm of force =  1.7474532e+19
 The mdp file is attached.

   Please help.

Madhumita Das


em.mdp
Description: Binary data
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[gmx-users] restart the mdrun with the checkpoint file

[xianqiang]

 Dear all,

I am trying to use the checkpoint file for the MDrun which war crashed.
However, the following error file was obtained in my log file:

Reading file md_0_2.tpr, VERSION 4.5.5 (single precision)

Reading checkpoint file state.cpt generated: Tue Nov  8 08:06:42 2011


starting mdrun 'Protein in water'
2000 steps,  2.0 ps (continuing from step 1685550,   1685.5 ps).
[a02c31n06.pdc.kth.se:20072] 7 more processes have sent help message 
help-mpi-btl-base.txt / btl:no-nics
[a02c31n06.pdc.kth.se:20072] Set MCA parameter "orte_base_help_aggregate" to 0 
to see all help / error messages

---
Program mdrun, VERSION 4.5.3
Source code file: ../../../gromacs-4.5.3/src/gmxlib/futil.c, line: 459

File input/output error:
state_step1714850.cpt
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"Good Music Saves your Soul" (Lemmy)

Error on node 0, will try to stop all the nodes
Halting parallel program mdrun on CPU 0 out of 8

gcq#311: "Good Music Saves your Soul" (Lemmy)

--
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 20073 on
node a02c31n06.pdc.kth.se exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--
~   
 

Anyone can help me with this problem?
Thanks so much,
Xianqiang


--

Xianqiang Sun


Email: xianqi...@theochem.kth.se
Division of Theoretical Chemistry and Biology
School of Biotechnology 
Royal Institute of Technology
S-106 91 Stockholm, Sweden  -- 
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[gmx-users] CygWin and Gromacs 4.5.5

[bhf70]

Help me.
I want to install Gromacs 4.5.5 with usage CygWin.
When I execute a command "make" I receive the error report:

numa_malloc.c:117: error: expected '> ' before ' Processor'
numa_malloc.c:117: error: expected '> ' before ' ProcNumber'
numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' asm '
or.
...
make [3]: *** [numa_malloc.lo] Error 1
make [3]: leaving directory '/cygdrive/.
gromacs4.5.5/src/gmxlib/thread_mpi'
make [3]: *** [install-recursive] Error 1
make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib'
make [3]: *** [install-recursive] Error 1
make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src'
make [3]: *** [install-recursive] Error 1

Where an error?


CygWin it is installed with packets:
Section "Devel"
- autoconf: Wrapper scripts for autoconf commands
- autoconf2.1: Stable version of the automatic configure script builder
- autoconf2.5: Development version of the automatic configure script builder
- automake1.9: a tool for generating GNU-compliant Makefiles
- binutils: The GNU assembler, linker and binary utilites
- gcc: A C compiler upgrade helper
- gcc-core: A C compiler
- gcc-g ++: A C ++ compiler
- gcc-g77: Fortran compiler
- gcc-mingw-core: Mingw32 support headers and libraries for GCC
- gcc-mingw-g ++: Mingw32 support headers and libraries for GCC A C ++
- gcc-mingw-g77: Mingw32 support headers and libraries for GCC Fortran
- libgcc1: GCC compiler support shared runtime
- libgdbm-devel: GNU dbm database routines (development)
- make: The GNU version of the ` make ` utility
- mingw-runtime: MinGW Runtime

Section "Interpreters"
- perl: Larry Wall ` s Practical Extracting and Report Language

Packet FFTW ver.3.2.2 is in addition compiled and installed

Trial setting Gromacs of 4.5.3 errors does not give.

The instruction on setting took here:
http://lists.groma cs.org/pipermail/gmx-users/2009-September/044792.html

The error arises only for version Gromacs 4.5.5


Igor


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[gmx-users] how to do remd with different tabulated potentials

[杜波]

dear teacher,

if i want to do remd  with different tabulated potentials.
how can i use the mdrun's   -table (-table table.xvg -tableb table.xvg )?

if it can also use like that,there is another question:
and how can i rename the tables name ( table_CR1_CR1: i rename
them table_CR1_CR10,table_CR1_CR11,table_CR1_CR12...,
i test this is wrong!!!
 )

thanks

regards,
PHD, Bo Du
Department of Polymer Science and Engineering,
School of Chemical Engineering and technology,
Tianjin University, Weijin Road 92, Nankai District 300072,
Tianjin City P. R. China
Tel/Fax: +86-22-27404303
E-mail: 2008d...@gmail.com 
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Re: [gmx-users] mdp file problem

[Justin A. Lemkul]

madhumita das wrote:


Hi GROMACS users,

i am in the midst of simulating  a protein in water.  I have 
modified  a residue  in my  pdb file at position  182,  using amber and 
then acpype.py.  But  after running  the energy minimization step,using  
em.mdp file  generated from acpype , following error comes.


Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps= 5000
Step=   17, Dmax= 1.5e-06 nm, Epot=  9.89827e+17 Fmax= inf, 
atom= 2700

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 18 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  9.8982703e+17
Maximum force =inf on atom 2700
Norm of force =  1.7474532e+19


An infinite force suggests severe atomic overlap.  Check the starting structure, 
paying close attention to atom 2700 and its surrounding environment.


-Justin

--


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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Re: [gmx-users] CygWin and Gromacs 4.5.5

[Szilárd Páll]

Hi,

There have been quite some discussion on the topic of GROMACS on
Cygwin so please search the mailing list for information.

Some of that information might have not gone into the wiki
(http://goo.gl/ALQuC) - especially that the page appears to be intact
for the last 7 months. [Which is a pity and it would be really much
appreciated if people in the future contribute back!!!]

Additionally, AFAIK you will get better performance if you compile
with MSVC which should be fairly easy if you use CMake - I'm not
entirely sure about this
though.
Cheers,
--
Szilárd



On Tue, Nov 8, 2011 at 12:41 PM,   wrote:
> Help me.
> I want to install Gromacs 4.5.5 with usage CygWin.
> When I execute a command "make" I receive the error report:
>
> numa_malloc.c:117: error: expected '> ' before ' Processor'
> numa_malloc.c:117: error: expected '> ' before ' ProcNumber'
> numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' asm '
> or.
> ...
> make [3]: *** [numa_malloc.lo] Error 1
> make [3]: leaving directory '/cygdrive/.
> gromacs4.5.5/src/gmxlib/thread_mpi'
> make [3]: *** [install-recursive] Error 1
> make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib'
> make [3]: *** [install-recursive] Error 1
> make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src'
> make [3]: *** [install-recursive] Error 1
>
> Where an error?
>
>
> CygWin it is installed with packets:
> Section "Devel"
> - autoconf: Wrapper scripts for autoconf commands
> - autoconf2.1: Stable version of the automatic configure script builder
> - autoconf2.5: Development version of the automatic configure script builder
> - automake1.9: a tool for generating GNU-compliant Makefiles
> - binutils: The GNU assembler, linker and binary utilites
> - gcc: A C compiler upgrade helper
> - gcc-core: A C compiler
> - gcc-g ++: A C ++ compiler
> - gcc-g77: Fortran compiler
> - gcc-mingw-core: Mingw32 support headers and libraries for GCC
> - gcc-mingw-g ++: Mingw32 support headers and libraries for GCC A C ++
> - gcc-mingw-g77: Mingw32 support headers and libraries for GCC Fortran
> - libgcc1: GCC compiler support shared runtime
> - libgdbm-devel: GNU dbm database routines (development)
> - make: The GNU version of the ` make ` utility
> - mingw-runtime: MinGW Runtime
>
> Section "Interpreters"
> - perl: Larry Wall ` s Practical Extracting and Report Language
>
> Packet FFTW ver.3.2.2 is in addition compiled and installed
>
> Trial setting Gromacs of 4.5.3 errors does not give.
>
> The instruction on setting took here:
> http://lists.groma cs.org/pipermail/gmx-users/2009-September/044792.html
>
> The error arises only for version Gromacs 4.5.5
>
>
> Igor
>
>
> --
> gmx-users mailing list    gmx-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
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Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)

[xi zhao]

When BASENAME.ORCAINFO has no coordinates of QMatoms, the mdrun showns "

Back Off! I just backed up md.log to ./#md.log.1#
Getting Loaded...
Reading file pyp_qm.tpr, VERSION 4.5.3 (double precision)
Loaded with Money
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 22
QMlevel: RHF/3-21G
/home/user/orca_x86_64_exe_r2131/home/user/orca_x86_64_exe_r2131...
orca initialised...
Back Off! I just backed up ener.edr to ./#ener.edr.1#
starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water'
500 steps,  0.5 ps.
Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp >> pyp_qm.out'
No atoms to convert in Cartesian2Internal" 
When BASENAME.ORCAINFO has coordinates of QMatoms, such as " 
!RKS BP RI SV(P) SV/J TightSCF Opt
* xyz -1 2
O 29.830  35.270  32.790
H 30.070  34.970  34.630
C 31.560  34.780  32.300
LA 31.740  34.840  30.880
...
mdrun shows :Back Off! I just backed up md.log to ./#md.log.1#
Getting Loaded...
Reading file pyp_qm.tpr, VERSION 4.5.3 (double precision)
Loaded with Money
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 22
QMlevel: RHF/3-21G
/home/user/orca_x86_64_exe_r2131/home/user/orca_x86_64_exe_r2131...
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.1#
starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water'
500 steps,  0.5 ps.
Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp >> pyp_qm.out'
   Unless this is specifically allowed this means that the basis set is not 
   available for this element - Aborting the run
---
Program mdrun_p, VERSION 4.5.3
Source code file: qm_orca.c, line: 409
Fatal error:
Call to '/home/user/orca_x86_64_exe_r2131/orca pyp_qm
 
how to write the  BASENAME.ORCAINFO?
how to deal with LA ? 

--- 11年11月8日，周二, Micha Ben Achim Kunze  写道：


发件人: Micha Ben Achim Kunze 
主题: Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)
收件人: gmx-users@gromacs.org
日期: 2011年11月8日,周二,下午4:19



I am not sure I understand exactly what you mean but this is all covered in 
Gerrit's QM/MM tutorials, I'd recommend you go through those. In the ORCA files 
there is no need to do anything with LAs, GMX will hand a file with the 
QMsubsystem to ORCA which includes the LA as hydrogens in your case I guess.

Cheers,
Micha
On 08/11/11 07:07, xi zhao wrote: 





Thank you for your suggest, my gromacs reinstalled: ./configure --
--without-qmmm-gaussian  --without-qmmm-orca 
  
when mpirun -np 1 mdrun_p -v -s pyp_qm.tpr, 

Back Off! I just backed up md.log to ./#md.log.1#
Getting Loaded...
Reading file pyp_qm.tpr, VERSION 4.5.3 (double precision)
Loaded with Money
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 22
QMlevel: RHF/3-21G
/home/user/orca_x86_64_exe_r2131/home/user/orca_x86_64_exe_r2131...
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.1#
starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water'
500 steps,  0.5 ps.
Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp >> pyp_qm.out'
   Unless this is specifically allowed this means that the basis set is not 
   available for this element - Aborting the run
---
Program mdrun_p, VERSION 4.5.3
Source code file: qm_orca.c, line: 409
Fatal error:
Call to '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp >> pyp_qm.out' failed
..
but a question raised:  how to deal with LA in the QMatoms in orca inputfile? 
using DA ( dummy atom in the ORCA) repaces LA in the QMatoms in the gromacs ?
please give me a suggestion!
Thank you!


--- 11年11月7日，周一, Micha Ben Achim Kunze  写道：


发件人: Micha Ben Achim Kunze 
主题: Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)
收件人: gmx-users@gromacs.org
日期: 2011年11月7日,周一,下午10:50



>From the output it looks like you forgot the --without-qmmm-gaussian flag 
>while compiling.

Micha
On 07/11/11 14:42, xi zhao wrote: 





When remove these lines, the errros still :Fatal error:
Invalid QMMM input: 1 groups 0 basissets and 0 methods;
when put something there, (
QMmethod =rhf;QMbasis =sto-3g), 

grompp_a -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o pyp_qm.tpr -maxwarn 10
 
mpirun -np 8 mdrun_a -v -s pyp_qm.tpr 
..
Back Off! I just backed up md.log to ./#md.log.7#
Getting Loaded...
Reading file pyp_qm.tpr, VERSION 4.5.3 (double precision)
Loaded with Money
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
there we go!
QM/MM calculation requested.
QM/MM calculation requested.
there we go!
there we go!
there we go!
there we go!
there we go!
there we go!
there we go!
Layer 0
nr of QM atoms 22
QMlevel: RHF/STO-3G
number of CPUs for

Re: [gmx-users] how to do remd with different tabulated potentials

[Mark Abraham]

On 8/11/2011 11:23 PM, ?? wrote:

dear teacher,

if i want to do remd  with different tabulated potentials.
how can i use the mdrun's   -table (-table table.xvg -tableb table.xvg )?

if it can also use like that,there is another question:
and how can i rename the tables name ( table_CR1_CR1: i rename
them table_CR1_CR10,table_CR1_CR11,table_CR1_CR12...,
i test this is wrong!!!
 )

thanks


Perhaps for this you need to use mdrun -multidir, which allows the files 
for each REMD replica to live in its own directory.  Now those directory 
names are provided to -multidir, and the filenames within each directory 
do not need to be patched with the replica ID.


Mark



regards,
PHD, Bo Du
Department of Polymer Science and Engineering,
School of Chemical Engineering and technology,
Tianjin University, Weijin Road 92, Nankai District 300072,
Tianjin City P. R. China
Tel/Fax: +86-22-27404303
E-mail: 2008d...@gmail.com  
>





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[gmx-users] barostat for gases

[Dr. Vitaly V. Chaban]

Could anybody please suggest a convenient compressibility value for MD
boxes of gases (at normal conditions)?

Thanks.

-- 
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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Re: [gmx-users] mdp file problem

[madhumita das]

Thanks Justin,

I must inform you that my pdb file has a modified cysteine residue having a
mercury atom attached to the sulphur atom next to the residue having the
atom 2700. Is the murcury atom creating any problem? I want to also know
can I use amber forcefield in GROMACS for pdb files of lipid?

On Tue, Nov 8, 2011 at 5:56 PM, Justin A. Lemkul  wrote:

>
>
> madhumita das wrote:
>
>>
>> Hi GROMACS users,
>>
>>i am in the midst of simulating  a protein in water.  I have modified
>>  a residue  in my  pdb file at position  182,  using amber and then
>> acpype.py.  But  after running  the energy minimization step,using  em.mdp
>> file  generated from acpype , following error comes.
>>
>> Steepest Descents:
>>   Tolerance (Fmax)   =  1.0e+03
>>   Number of steps= 5000
>> Step=   17, Dmax= 1.5e-06 nm, Epot=  9.89827e+17 Fmax= inf, atom=
>> 2700
>> Stepsize too small, or no change in energy.
>> Converged to machine precision,
>> but not to the requested precision Fmax < 1000
>>
>> Double precision normally gives you higher accuracy.
>>
>> writing lowest energy coordinates.
>>
>> Steepest Descents converged to machine precision in 18 steps,
>> but did not reach the requested Fmax < 1000.
>> Potential Energy  =  9.8982703e+17
>> Maximum force =inf on atom 2700
>> Norm of force =  1.7474532e+19
>>
>
> An infinite force suggests severe atomic overlap.  Check the starting
> structure, paying close attention to atom 2700 and its surrounding
> environment.
>
> -Justin
>
> --
> ==**==
>
> 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/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
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> Can't post? Read 
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Re: [gmx-users] mdp file problem

[Justin A. Lemkul]

madhumita das wrote:

Thanks Justin,

I must inform you that my pdb file has a modified cysteine residue 
having a mercury atom attached to the sulphur atom next to the residue 
having the atom 2700. Is the murcury atom creating any problem? I want 


Probably.  Parameterizing such a species properly is not trivial, if it can even 
be done in a non-polarizable MM force field.


http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species


to also know can I use amber forcefield in GROMACS for pdb files of lipid?



Lipids probably aren't built in, but could potentially be added if you provide 
the proper parameters.  CHARMM is probably a better choice.  CHARMM27 is built 
into Gromacs already, and CHARMM36 is available as a download from the website.


-Justin

On Tue, Nov 8, 2011 at 5:56 PM, Justin A. Lemkul > wrote:




madhumita das wrote:


Hi GROMACS users,

   i am in the midst of simulating  a protein in water.  I have
modified  a residue  in my  pdb file at position  182,  using
amber and then acpype.py.  But  after running  the energy
minimization step,using  em.mdp file  generated from acpype ,
following error comes.

Steepest Descents:
  Tolerance (Fmax)   =  1.0e+03
  Number of steps= 5000
Step=   17, Dmax= 1.5e-06 nm, Epot=  9.89827e+17 Fmax=
inf, atom= 2700

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 18 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  9.8982703e+17
Maximum force =inf on atom 2700
Norm of force =  1.7474532e+19


An infinite force suggests severe atomic overlap.  Check the
starting structure, paying close attention to atom 2700 and its
surrounding environment.

-Justin

-- 
==__==


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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 before posting!
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.
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--


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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Re: [gmx-users] barostat for gases

[Krzysztof Kuczera]

The ideal gas result is -(1/V)(dV/dp)_T = 1/p  , so I suppose the value 
should be = 1.0  bar-1

under standard conditions
Krzysztof

On 11/8/11 10:51 AM, Dr. Vitaly V. Chaban wrote:

Could anybody please suggest a convenient compressibility value for MD
boxes of gases (at normal conditions)?

Thanks.




--
Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html



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Re: [gmx-users] CygWin and Gromacs 4.5.5

[bhf70]

I have read and have carried out the instruction on the given page.
The error arises again.

Igor


В письме от Втр, 08 Ноя 2011, 16:35 Szilárd Páll пишет:
> Hi,
>
>
> There have been quite some discussion on the topic of GROMACS on
> Cygwin so please search the mailing list for information.
>
>
> Some of that information might have not gone into the wiki
> (http://goo.gl/ALQuC) - especially that the page appears to be intact
> for the last 7 months. [Which is a pity and it would be really much
> appreciated if people in the future contribute back!!!]
>
> Additionally, AFAIK you will get better performance if you compile
> with MSVC which should be fairly easy if you use CMake - I'm not entirely
> sure about this though. Cheers,
> --
> Szilárd
>
>
>
>
> On Tue, Nov 8, 2011 at 12:41 PM,   wrote:
>
>> Help me.
>> I want to install Gromacs 4.5.5 with usage CygWin.
>> When I execute a command "make" I receive the error report:
>>
>>
>> numa_malloc.c:117: error: expected '> ' before ' Processor'
>> numa_malloc.c:117: error: expected '> ' before ' ProcNumber'
>> numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' asm '
>> or. ...
>> make [3]: *** [numa_malloc.lo] Error 1 make [3]: leaving directory
>> '/cygdrive/.
>> gromacs4.5.5/src/gmxlib/thread_mpi' make [3]: *** [install-recursive]
>> Error 1
>> make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib'
>> make [3]: *** [install-recursive] Error 1 make [3]: leaving directory
>> '/cygdrive/. gromacs4.5.5/src'
>> make [3]: *** [install-recursive] Error 1
>>
>> Where an error?
>>
>>
>>
>> CygWin it is installed with packets:
>> Section "Devel"
>> - autoconf: Wrapper scripts for autoconf commands
>> - autoconf2.1: Stable version of the automatic configure script builder
>> - autoconf2.5: Development version of the automatic configure script
>> builder - automake1.9: a tool for generating GNU-compliant Makefiles
>> - binutils: The GNU assembler, linker and binary utilites
>> - gcc: A C compiler upgrade helper
>> - gcc-core: A C compiler
>> - gcc-g ++: A C ++ compiler
>> - gcc-g77: Fortran compiler
>> - gcc-mingw-core: Mingw32 support headers and libraries for GCC
>> - gcc-mingw-g ++: Mingw32 support headers and libraries for GCC A C ++
>> - gcc-mingw-g77: Mingw32 support headers and libraries for GCC Fortran
>> - libgcc1: GCC compiler support shared runtime
>> - libgdbm-devel: GNU dbm database routines (development)
>> - make: The GNU version of the ` make ` utility
>> - mingw-runtime: MinGW Runtime
>>
>>
>> Section "Interpreters"
>> - perl: Larry Wall ` s Practical Extracting and Report Language
>>
>>
>> Packet FFTW ver.3.2.2 is in addition compiled and installed
>>
>>
>> Trial setting Gromacs of 4.5.3 errors does not give.
>>
>>
>> The instruction on setting took here:
>> http://lists.groma cs.org/pipermail/gmx-users/2009-September/044792.html
>>
>>
>> The error arises only for version Gromacs 4.5.5
>>
>>
>>
>> Igor
>>
>>
>>
>> --
>> gmx-users mailing list    gmx-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
>>
>>
> --
> 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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Re: [gmx-users] A question about deuteriu order parameters graph

[Alex Jemulin]

Dear Javier

Here is mdp file for MD run

title        = cxcr7-DPPC Production MD 
; 
Run parameters

integrator    = md        ; leap-frog integrator

nsteps        = 50    ; 2 * 50 = 1000 ps (1 ns)

dt            = 0.002        ; 2 fs
; 
Output control

nstxout        = 1000        ; save coordinates every 2 ps

nstvout        = 1000        ; save velocities every 2 ps

nstxtcout    = 1000        ; xtc compressed trajectory output every 2 ps

nstenergy    = 1000        ; save energies every 2 p

nstlog        = 1000        ; update log file every 2 ps

; Bond parameters

continuation    = yes            ; Restarting after NPT 

constraint_algorithm = lincs    ; holonomic 
constraints 
constraints    = all-bonds        ; all bonds (even heavy atom-H bonds) 
constrained

lincs_iter    = 1            ; accuracy of LINCS

lincs_order    = 4            ; also related to accuracy

; Neighborsearching

ns_type        = grid        ; search neighboring grid cels

nstlist        = 5            ; 10 fs

rlist        = 1.2        ; short-range neighborlist cutoff (in nm)

rcoulomb    = 1.2        ; short-range electrostatic cutoff (in nm)

rvdw        = 1.2        ; short-range van der Waals cutoff (in nm)
; 
Electrostatics

coulombtype    = PME        ; Particle Mesh Ewald for long-range electrostatics

pme_order    = 4            ; cubic interpolation

fourierspacing    = 0.16        ; grid spacing for FFT

; Temperature coupling is on

tcoupl        = Nose-Hoover            ; More accurate thermostat

tc-grps        = Protein DPPC    SOL_NA    ; three coupling groups - more 
accurate

tau_t        = 0.5    0.5    0.5        ; time constant, in ps

ref_t        = 323     323    323        ; reference temperature, one for 
each group, in K
; 
Pressure coupling is on

pcoupl        = Parrinello-Rahman        ; Pressure coupling on in NPT

pcoupltype    = semiisotropic            ; uniform scaling of x-y box vectors, 
independent 
z
tau_p        = 2.0                ; time constant, in ps

ref_p        = 1.0    1.0            ; reference pressure, x-y, z (in bar)

compressibility = 4.5e-5    4.5e-5    ; isothermal compressibility, bar^-1
; 
Periodic boundary conditions

pbc            = xyz        ; 3-D PBC
; 
Dispersion correction

DispCorr    = EnerPres    ; account for cut-off vdW scheme
; 
Velocity generation

gen_vel        = no        ; Velocity generation is off

; COM motion removal

; These options remove motion of the protein/bilayer relative to the 
solvent/ions

nstcomm = 1

comm-mode   = Linear

comm-grps   = Protein_DPPC SOL_NA 

Here are some graphs I made after MD run:
g_energy -f md_0_1.edr -o temperature_MD.xvg
http://www.freeimagehosting.net/ca04e

g_energy -f md_0_1.edr -o pressione_MD.xvg
http://www.freeimagehosting.net/d3387


g_energy -f md_0_1.edr -o totenergia_MD.xvg
http://www.freeimagehosting.net/108a7


Here are commands for calculating deuterium order parameters

make_ndx -f md_0_1.tpr -o sn1.ndx
> a C34 
> a C36 
> a C37 
> a C38 
... 
> a C50 
> del 0-21 
> q 

g_order -s md_0_1.tpr -f md_0_1.xtc -n sn1.ndx -d z -od deuter_sn1.xvg

make_ndx -f md_0_1.tpr -o sn2.ndx
carbons  C17-C31 
del 0-21 
q
g_order -s md_0_1.tpr -f md_0_1.xtc -n sn2.ndx -d z -od deuter_sn2.xvg


Thank your very much for your support

Bests




Da: Javier Cerezo 
A: gmx-users@gromacs.org
Inviato: Martedì 8 Novembre 2011 9:45
Oggetto: Re: [gmx-users] A question about deuteriu order parameters graph

Hi Alex

Deuterium order parameter is a property related to the relative orientation of 
molecular axis taking the bilayer normal as reference. How to use them to 
extract useful structural information is a matter of how you interpret the 
values regarding their definition (see e.g. Egberts and Berendsen [J. Chem. 
Phys.(1988), vol 89, 3718] or Heller et al [J. Phys. Chem. (1993), vol 97, 
8343]). In general, by comparing order parameters of different systems you can 
have some hints about the phase or ordering of your different systems and how 
it may change (for example at different temperature or after insertion of a 
membrane protein).

Morover, the usefulness of this paramenter mainly comes from the fact that they 
are readily available from simulations and thus can be used to validate your 
methodology. Concretely, experimental information about the deuterium order 
parameter (Scd, the one you reported) is spread over the scientific literature 
about membranes (see e.g. the series of papers from the J.F Nagle's group) and 
it is the deuterium order parameter commonly reported in MD simulations. For 
the case of DPPC you can take for example the ones from Petrache et al 
[Biophys. J (2000), vol 79, 3172] and Douliez et al [Biophys. J. (1995), vol 
68, 1727]. Take into account that GROMACS g_order tool just numerate your atoms 
in the order the order parameters are calculated: the first Scd comes from the 
second atom in the in

[gmx-users] where is Coul-LR?

[Yun Shi]

Hello all,

I understand that setting rcoulomb > rlist should give me Coul-LR from the
.edr file. But I set rcoulomb = rlist since PME was used to calculate long
range electrostatic interactions, and when I tried g_energy, I only have:

58  Coul-SR:Protein-LIG
 59  LJ-SR:Protein-LIG   60
LJ-LR:Protein-LIG
 61  Coul-14:Protein-LIG 62
LJ-14:Protein-LIG

So where is Coul-LR? How should I get it?

Thanks,
Yun
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Re: [gmx-users] where is Coul-LR?

[Justin A. Lemkul]

Yun Shi wrote:

Hello all,

I understand that setting rcoulomb > rlist should give me Coul-LR from 
the .edr file. But I set rcoulomb = rlist since PME was used to 
calculate long range electrostatic interactions, and when I tried 
g_energy, I only have:


58  Coul-SR:Protein-LIG  
 59  LJ-SR:Protein-LIG   60  
LJ-LR:Protein-LIG
 61  Coul-14:Protein-LIG 62  
LJ-14:Protein-LIG


So where is Coul-LR? How should I get it?



As you correctly noted, Coul-LR is produced only when rcoulomb > rlist.  You 
cannot use such settings with PME.


-Justin


Thanks,
Yun



--


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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Re: [gmx-users] CygWin and Gromacs 4.5.5

[Mark Abraham]

On 8/11/2011 11:35 PM, Szilárd Páll wrote:

Hi,

There have been quite some discussion on the topic of GROMACS on
Cygwin so please search the mailing list for information.


Actually I don't think this issue has been addressed. Some NUMA-aware 
thread_mpi stuff does not work under Cygwin, and code added since 4.5.4 
assumes that it does. I can find no reason to support that assumption.


To work around, use configure --disable-threads.



Some of that information might have not gone into the wiki
(http://goo.gl/ALQuC) - especially that the page appears to be intact
for the last 7 months. [Which is a pity and it would be really much
appreciated if people in the future contribute back!!!]

Additionally, AFAIK you will get better performance if you compile
with MSVC which should be fairly easy if you use CMake - I'm not
entirely sure about this


I'd be surprised. Why should MSVC outperform gcc?

Mark


though.
Cheers,
--
Szilárd



On Tue, Nov 8, 2011 at 12:41 PM,  wrote:

Help me.
I want to install Gromacs 4.5.5 with usage CygWin.
When I execute a command "make" I receive the error report:

numa_malloc.c:117: error: expected '>  ' before ' Processor'
numa_malloc.c:117: error: expected '>  ' before ' ProcNumber'
numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' asm '
or.
...
make [3]: *** [numa_malloc.lo] Error 1
make [3]: leaving directory '/cygdrive/.
gromacs4.5.5/src/gmxlib/thread_mpi'
make [3]: *** [install-recursive] Error 1
make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib'
make [3]: *** [install-recursive] Error 1
make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src'
make [3]: *** [install-recursive] Error 1

Where an error?


CygWin it is installed with packets:
Section "Devel"
- autoconf: Wrapper scripts for autoconf commands
- autoconf2.1: Stable version of the automatic configure script builder
- autoconf2.5: Development version of the automatic configure script builder
- automake1.9: a tool for generating GNU-compliant Makefiles
- binutils: The GNU assembler, linker and binary utilites
- gcc: A C compiler upgrade helper
- gcc-core: A C compiler
- gcc-g ++: A C ++ compiler
- gcc-g77: Fortran compiler
- gcc-mingw-core: Mingw32 support headers and libraries for GCC
- gcc-mingw-g ++: Mingw32 support headers and libraries for GCC A C ++
- gcc-mingw-g77: Mingw32 support headers and libraries for GCC Fortran
- libgcc1: GCC compiler support shared runtime
- libgdbm-devel: GNU dbm database routines (development)
- make: The GNU version of the ` make ` utility
- mingw-runtime: MinGW Runtime

Section "Interpreters"
- perl: Larry Wall ` s Practical Extracting and Report Language

Packet FFTW ver.3.2.2 is in addition compiled and installed

Trial setting Gromacs of 4.5.3 errors does not give.

The instruction on setting took here:
http://lists.groma cs.org/pipermail/gmx-users/2009-September/044792.html

The error arises only for version Gromacs 4.5.5


Igor


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[gmx-users] newbie question about GROMACS input files

[Markus K. Dahlgren]

Hi all!

I am new to the Gromacs mailing list and just started looking into Gromacs for
MD simulations. I have been working on converting BOSS output into automatic
NAMD input for small molecule ligands and now want to create a similar program
for Gromacs input. I have a question regarding the input files, as I find the
large number of files confusing.

What is the required files to start a Gromacs simulation? Using pdb2gmx you need
a pdb file. To get the parameters, ffbonded.itp, ffnonbonded.itp, atomtypes.atp
and *.rtp are needed? Is that all the files needed if these files completely
describe the input molecules? Also, does the new parameters for the ligand need
to go into the existing parameter files inside the XXX.ff folder? Or how can new
*.itp, *.rtp and *atp files be defined and called upon by pdb2gmx?

I also read about the topology file in the manual. If a topology file would be
written by the program, what other files are needed? The topology would have
all atomtypes, names, charges, bonds, angles, and dihedrals. Would it be enough
to supply a nonbonded.itp file together with the *.top file and the pdb file?

Finally I have a question about the *.gro files. Are they always needed when
starting a simulation? For a new simulation, the last three columns (vx, vy,
vz) can be left out?

Sorry about asking about such trivial matters, but the number of files was
confusing and I was not sure what files were needed if I would bypass the
pdb2gmx step and write the topology file directly.

Thanks in advance for any insight you can offer.

Best,
Markus



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Re: [gmx-users] newbie question about GROMACS input files

[Justin A. Lemkul]

Markus K. Dahlgren wrote:

Hi all!

I am new to the Gromacs mailing list and just started looking into Gromacs for
MD simulations. I have been working on converting BOSS output into automatic
NAMD input for small molecule ligands and now want to create a similar program
for Gromacs input. I have a question regarding the input files, as I find the
large number of files confusing.

What is the required files to start a Gromacs simulation? Using pdb2gmx you need


The required files are a coordinate file (many formats are acceptable), a 
topology (.top), and simulation instructions (.mdp).



a pdb file. To get the parameters, ffbonded.itp, ffnonbonded.itp, atomtypes.atp
and *.rtp are needed? Is that all the files needed if these files completely
describe the input molecules? Also, does the new parameters for the ligand need
to go into the existing parameter files inside the XXX.ff folder? Or how can new
*.itp, *.rtp and *atp files be defined and called upon by pdb2gmx?



These files are only needed by pdb2gmx.  In theory, you don't need them for 
anything if you write a topology by hand.  For instance, for a ligand, it 
doesn't make much sense to incorporate all the new parameters into the 
highest-level force field files just to have pdb2gmx write the same information 
out; just create an .itp for whatever small molecule you have.  pdb2gmx is only 
really useful for macromolecules constructed of smaller building blocks.



I also read about the topology file in the manual. If a topology file would be
written by the program, what other files are needed? The topology would have
all atomtypes, names, charges, bonds, angles, and dihedrals. Would it be enough
to supply a nonbonded.itp file together with the *.top file and the pdb file?



The ffnonbonded.itp is unnecessary if everything is supplied in the .top - you 
can see how the topology is completely constructed by running through one of the 
many tutorial systems and getting a post-processed topology from grompp -pp.



Finally I have a question about the *.gro files. Are they always needed when
starting a simulation? For a new simulation, the last three columns (vx, vy,
vz) can be left out?



Many coordinate files can be used; a .gro is not specifically required.  You are 
correct about the velocities.  Use "gen_vel = yes" to start a new simulation if 
you do not have velocities you wish to preserve.



Sorry about asking about such trivial matters, but the number of files was
confusing and I was not sure what files were needed if I would bypass the
pdb2gmx step and write the topology file directly.



If you write the topology by hand or with some external software, then you can 
bypass almost everything.


-Justin

--


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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Re: [gmx-users] newbie question about GROMACS input files

[Mark Abraham]

On 9/11/2011 10:08 AM, Markus K. Dahlgren wrote:

Hi all!

I am new to the Gromacs mailing list and just started looking into Gromacs for
MD simulations. I have been working on converting BOSS output into automatic
NAMD input for small molecule ligands and now want to create a similar program
for Gromacs input. I have a question regarding the input files, as I find the
large number of files confusing.

What is the required files to start a Gromacs simulation? Using pdb2gmx you need
a pdb file. To get the parameters, ffbonded.itp, ffnonbonded.itp, atomtypes.atp
and *.rtp are needed?


To generate a topology pdb2gmx requires .atp and .rtp files, and maybe 
some other stuff depending on what functionality is required. To use a 
topology, grompp requires that the #include statements generated by 
pdb2gmx make sense, so the .itp files are only then required. Updating 
residuetypes.dat can be wise.



  Is that all the files needed if these files completely
describe the input molecules? Also, does the new parameters for the ligand need
to go into the existing parameter files inside the XXX.ff folder? Or how can new
*.itp, *.rtp and *atp files be defined and called upon by pdb2gmx?


You can make a new local copy of the xxx.ff folder and modify that. 
However, it is more work to create an .rtp entry for a small molecule 
and use pdb2gmx than it is to write a molecule.itp file directly (see 
example in Chapter 5 of the manual). Such an .itp file can probably have 
[nonbond_params] or [atomtypes] fields in it, or implicitly refer to a 
modified ffnonbonded.itp.




I also read about the topology file in the manual. If a topology file would be
written by the program, what other files are needed? The topology would have
all atomtypes, names, charges, bonds, angles, and dihedrals. Would it be enough
to supply a nonbonded.itp file together with the *.top file and the pdb file?


Yes. Note that parameters for bonded interactions can be provided 
directly in the .itp where the interaction is defined, rather than by 
reference to a bonded interaction type entry.




Finally I have a question about the *.gro files. Are they always needed when
starting a simulation? For a new simulation, the last three columns (vx, vy,
vz) can be left out?


A coordinate file is required, but its format can be to suit your 
convenience. Particularly if you are generating velocities, the velocity 
values can be irrelevant.




Sorry about asking about such trivial matters, but the number of files was
confusing and I was not sure what files were needed if I would bypass the
pdb2gmx step and write the topology file directly.


You can.

Mark



Thanks in advance for any insight you can offer.

Best,
Markus





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[gmx-users] ORCA and dummy atom in the gromacs

[xi zhao]

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. 
When BASENAME.ORCAINFO has no coordinates of QMatoms, the mdrun showns "
Back Off! I just backed up md.log to ./#md.log.1#
Getting Loaded...
Reading file pyp_qm.tpr, VERSION 4.5.3 (double precision)
Loaded with Money
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 22
QMlevel: RHF/3-21G
/home/user/orca_x86_64_exe_r2131/home/user/orca_x86_64_exe_r2131...
orca initialised...
Back Off! I just backed up ener.edr to ./#ener.edr.1#
starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water'
500 steps,  0.5 ps.
Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp >> pyp_qm.out'
No atoms to convert in Cartesian2Internal" 
………
When BASENAME.ORCAINFO has coordinates of QMatoms, such as " 
!RKS BP RI SV(P) SV/J TightSCF Opt
* xyz -1 2
O 29.830  35.270  32.790
H 30.070  34.970  34.630
C 31.560  34.780  32.300
LA 31.740  34.840  30.880
...
mdrun shows :Back Off! I just backed up md.log to ./#md.log.1#
Getting Loaded...
Reading file pyp_qm.tpr, VERSION 4.5.3 (double precision)
Loaded with Money
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 22
QMlevel: RHF/3-21G
/home/user/orca_x86_64_exe_r2131/home/user/orca_x86_64_exe_r2131...
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.1#
starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water'
500 steps,  0.5 ps.
Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp >> pyp_qm.out'
   Unless this is specifically allowed this means that the basis set is not 
   available for this element - Aborting the run
---
Program mdrun_p, VERSION 4.5.3
Source code file: qm_orca.c, line: 409
Fatal error:
Call to '/home/user/orca_x86_64_exe_r2131/orca pyp_qm
 
how to write the BASENAME.ORCAINFO?
how to deal with LA in the gromacs for ORCA calculation?
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Re: [gmx-users] CygWin and Gromacs 4.5.5

[Roland Schulz]

On Tue, Nov 8, 2011 at 5:59 PM, Mark Abraham wrote:

> On 8/11/2011 11:35 PM, Szilárd Páll wrote:
> > Additionally, AFAIK you will get better performance if you compile
> > with MSVC which should be fairly easy if you use CMake - I'm not
> > entirely sure about this
>
> I'd be surprised. Why should MSVC outperform gcc?
>
The file performance is horrible with cygwin (even much slower than a
virtual machine). But this should only be important for analysis. For
simulation I agree that the performance should be as good  (I don't know
about NUMA) .

Roland

>
> Mark
>
> > though.
> > Cheers,
> > --
> > Szilárd
> >
> >
> >
> > On Tue, Nov 8, 2011 at 12:41 PM,  wrote:
> >> Help me.
> >> I want to install Gromacs 4.5.5 with usage CygWin.
> >> When I execute a command "make" I receive the error report:
> >>
> >> numa_malloc.c:117: error: expected '>  ' before ' Processor'
> >> numa_malloc.c:117: error: expected '>  ' before ' ProcNumber'
> >> numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' asm '
> >> or.
> >> ...
> >> make [3]: *** [numa_malloc.lo] Error 1
> >> make [3]: leaving directory '/cygdrive/.
> >> gromacs4.5.5/src/gmxlib/thread_mpi'
> >> make [3]: *** [install-recursive] Error 1
> >> make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib'
> >> make [3]: *** [install-recursive] Error 1
> >> make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src'
> >> make [3]: *** [install-recursive] Error 1
> >>
> >> Where an error?
> >>
> >>
> >> CygWin it is installed with packets:
> >> Section "Devel"
> >> - autoconf: Wrapper scripts for autoconf commands
> >> - autoconf2.1: Stable version of the automatic configure script builder
> >> - autoconf2.5: Development version of the automatic configure script
> builder
> >> - automake1.9: a tool for generating GNU-compliant Makefiles
> >> - binutils: The GNU assembler, linker and binary utilites
> >> - gcc: A C compiler upgrade helper
> >> - gcc-core: A C compiler
> >> - gcc-g ++: A C ++ compiler
> >> - gcc-g77: Fortran compiler
> >> - gcc-mingw-core: Mingw32 support headers and libraries for GCC
> >> - gcc-mingw-g ++: Mingw32 support headers and libraries for GCC A C ++
> >> - gcc-mingw-g77: Mingw32 support headers and libraries for GCC Fortran
> >> - libgcc1: GCC compiler support shared runtime
> >> - libgdbm-devel: GNU dbm database routines (development)
> >> - make: The GNU version of the ` make ` utility
> >> - mingw-runtime: MinGW Runtime
> >>
> >> Section "Interpreters"
> >> - perl: Larry Wall ` s Practical Extracting and Report Language
> >>
> >> Packet FFTW ver.3.2.2 is in addition compiled and installed
> >>
> >> Trial setting Gromacs of 4.5.3 errors does not give.
> >>
> >> The instruction on setting took here:
> >> http://lists.groma
> cs.org/pipermail/gmx-users/2009-September/044792.html
> >>
> >> The error arises only for version Gromacs 4.5.5
> >>
> >>
> >> Igor
> >>
> >>
> >> --
> >> 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!
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> >> www interface or send it to gmx-users-requ...@gromacs.org.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
>
>
>
>


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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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