Re:Re: [gmx-users] MDRun -append error

[xianqiang]

Hi Roland,

Thanks for your reply. My log files are located in the same directory with 
''traj.xtc', and the log files are readable by gromacs.

I have just find out the solution for my problem. That is because there were 
also two backup log files named '#md_0_1.log#' and '#md_0_1.edr#' corresponding 
to 'md_0_1.log' and 'md_0_1.edr'. These two files were generated for a trial 
run. After removing the two files ('#md_0_1.log#' and '#md_0_1.edr#), gromacs 
can restart successfully.

Thanks for your reply!
best regards
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  

在 2011-11-17 09:12:25，"Roland Schulz"  写道：



On Wed, Nov 16, 2011 at 4:11 PM, xianqiang  wrote:

 Hi, all

I just restart a simulation with 'mpirun -np 8 mdrun -pd yes -s md_0_1.tpr -cpi 
state.cpt -append'

However, the following error appears:


Output file appending has been requested,
but some output files listed in the checkpoint file state.cpt
are not present or are named differently by the current program:
output files present: traj.xtc
output files not present or named differently: md_0_1.log md_0_1.edr

---
Program mdrun, VERSION 4.5.3
Source code file: ../../../gromacs-4.5.3/src/gmxlib/checkpoint.c, line: 2139

Fatal error:
File appending requested, but only 1 of the 3 output files are present
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


The two files which can not be found were located in the same directory with 
'traj.xtc', and why they can not be found by gromacs?

Maybe they are not readable? Can you look at the log file (e.g. using "less")?


Roland
 

Thanks and best regards,
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] Strange problem.complex out of Box after EM

[Saba Ferdous]

Dear Gromacs users

I am trying to simulate a protein complex. That complex has been obtained
after protein-protein docking.

I have geneated topology, defined box and solvate, added ions successfully.
My complex is centered in box.

but when I performed Energy minimization then my protein complex comes out
of box from one side.

can any body help me in fixing this problem so that i could proceed towards
equilibrium steps..

Many thanks with anticipation


Regards
Saba


-- 
Saba Ferdous
Research Scholar (M. Phil)
National Center for Bioinformatics
Quaid-e-Azam University, Islamabad
Pakistan
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Re: [gmx-users] gromacs/mopac compilation: linking libmopac

[Javier Cerezo]

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 calls. So I 
capped this loop (is should end at line 89), so that now it looks like:]

Line 35:IF(ICALCN.NE.NUMCAL) THEN
Line 36:   ICALCN=NUMCAL
Line 37(new):   ENDIF [this was moved from line 89]

And now I could run gromacs/mopac without errors. I guess with another 
compiler, this problem will not arise, but at least here is a solution 
for (standard?) gfortran in a x86_64 system


Javier



El 10/11/11 14:35, Javier Cerezo escribió:

Hi all

I am trying to compi

[gmx-users] Regarding TIP4P structure

[Ravi Kumar Venkatraman]

Dear all,
 Could anybody send me the link for getting the tip4p tip3p and
tip5p single water structure in gro/pdb or in anyother format.

Thank you.

*With Regards,
Ravi Kumar Venkatraman,
IPC Dept., IISc,
Bangalore, INDIA.

+91-9686933963.*
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[gmx-users] gromacs/mopac compilation: linking libmopac (Javier Cerezo)

[Gerrit Groenhof]

ortran/folder> ar rcv libmopac.a *.o;ranlib libmopac.a
>> javier@mopac/fortran/folder> cp libmopac.a ~/lib
>> 
>> [in gromacs folder]
>> javier@gromacs/folder> ./configure --prefix 
>> /home/cerezo/Programas/gromacs-4.5.5_with_mopac/ --with-qmmm-mopac 
>> --without-qmmm-gaussian  --disable-threads --disable-shared 
>> LDFLAGS="-L/home/cerezo/lib" CPPFLAGS="-DUSE_MOPAC" LIBS="-lmopac"
>> javier@gromacs/folder> make -j 4
>> 
>> This time I also get "undefined reference errors", but related to f2c 
>> funtions:
>> +timout.c0x105:)(:. textundefined+ 0x3c8reference) :to  undefined` 
>> do_fioreference'
>> totimer.c :`(do_fio.'text
>> 
>> In this case, do I need to include the f2c.h file somewhere in the 
>> gromacs qmmm interface code?
>> 
>> Could someone point me out where I'm mistaking and what should I do to 
>> complete the installation?
>> 
>> Thanks
>> 
>> Javier
>> 
>> 
> 
> -- 
> Javier CEREZO BASTIDA
> PhD Student
> Physical Chemistry
> Universidad de Murcia
> Murcia (Spain)
> Tlf.(+34)868887434
> 
> 
> 
> --
> 
> Message: 4
> Date: Thu, 17 Nov 2011 15:51:53 +0530
> From: Ravi Kumar Venkatraman 
> Subject: [gmx-users] Regarding TIP4P structure
> To: gmx-users@gromacs.org
> Message-ID:
>   
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear all,
> Could anybody send me the link for getting the tip4p tip3p and
> tip5p single water structure in gro/pdb or in anyother format.
> 
> Thank you.
> 
> *With Regards,
> Ravi Kumar Venkatraman,
> IPC Dept., IISc,
> Bangalore, INDIA.
> 
> +91-9686933963.*
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> End of gmx-users Digest, Vol 91, Issue 117
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Re: [gmx-users] gromacs/mopac compilation: linking libmopac (Javier Cerezo)

[Javier Cerezo]

what should I do to
complete the installation?

Thanks

Javier



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



--

Message: 4
Date: Thu, 17 Nov 2011 15:51:53 +0530
From: Ravi Kumar Venkatraman
Subject: [gmx-users] Regarding TIP4P structure
To: gmx-users@gromacs.org
Message-ID:

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

Dear all,
 Could anybody send me the link for getting the tip4p tip3p and
tip5p single water structure in gro/pdb or in anyother format.

Thank you.

*With Regards,
Ravi Kumar Venkatraman,
IPC Dept., IISc,
Bangalore, INDIA.

+91-9686933963.*
-- next part --
An HTML attachment was scrubbed...
URL: 
http://lists.gromacs.org/pipermail/gmx-users/attachments/2017/4840f654/attachment.html

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End of gmx-users Digest, Vol 91, Issue 117
**


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

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[gmx-users] Regarding cosine content

[bipin singh]

Hello all,

I have done PCA from 50ns long trajectory for two similar proteins
(length 180 aa and RMSD 0.2 A).
The equilibration time and final simulation condition were identical
for both the protein.
But when I checked the cosine content for PC1 for both proteins they
were 0.9 and 0.5 respectively.
What can be the reason for this huge difference in cosine content of
the two proteins ?


-- 
---
Regards,
Bipin Singh
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Re: [gmx-users] Strange problem.complex out of Box after EM

[Justin A. Lemkul]

Saba Ferdous wrote:

Dear Gromacs users

I am trying to simulate a protein complex. That complex has been 
obtained after protein-protein docking.


I have geneated topology, defined box and solvate, added ions 
successfully. My complex is centered in box.


but when I performed Energy minimization then my protein complex comes 
out of box from one side.


can any body help me in fixing this problem so that i could proceed 
towards equilibrium steps..




There is no problem.  It is odd that EM would cause periodicity issues, but 
suggests that your protein is not centered properly or that your box is not 
large enough to accommodate it.  There may be some inconvenience for 
visualization (which can be fixed), but there is no such thing as "outside" in a 
periodic system.


http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-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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[gmx-users] Re: Umbrella Sampling - Justin tutorial

[Steven Neumann]

Hi Justin,

I am sorry for so many questions but I do not understand something.
First we run the simulation of pulling Chain A from ChainB with constant
force (pull_k1=1000) and constant velocity of pulling (pull_rate1=0.01) We
extract windows as we discussed and then run simulations with those
configurations as a starting point. I saw the trajectory of one of these
simulations and it looks like normal MD simulation. My question is: Why do
we have in mdp file still pull code as we do not pull protein chain any
more? Pull rate is set to zero but force is still applied... why? Is this
code just used to extract pullf.xvg and pullx.xvg which does not change too
much?
I would appreciate the explanation as without undesratnding the basics its
not good to do any simulation like this.

Thank you

Steven




Are my questions to trivial or noones knows? Please, help!

On Wed, Nov 16, 2011 at 9:31 AM, Steven Neumann wrote:

> Hi GMX Users,
>
> I am doing Justin tutorial of Umbrella sampling. I have just finished
> continous pulling of chainA from the reference chainB. I have some
> questions. I looked at the trajectory of pulling and it has began with
> dissociating residue 27Alanine from the ChainB following 26, 25, 24...1. My
> question is why? As you apply pulling with the constant force to the COM of
> the whole chain why does it start with terminal residue following then one
> by one? Why not the middle one or any other?
>
> The second thing I would like to extract starting configurations from from
> my pulling. Till frame 189 the COM varies from 0.49 to 0.56 - makes sense
> as the ChainA is still within ChainB. I would like to use configurations:
>
> 0 - 0.50
> 50 - 0.52
> 100 - 0.51
> 150 - 0.51
> 200 - 0.62
> 250 - 2.21
> 
> 500 - 5.48
>
> My question is: Do I have to use exactly the same e.g. 0.2 nm spacing or
> this configuration above is ok? Can the spacing in nm vary?
> And the last thing - is it required to use frames till 189 as the COM
> varies in this area?
>
> Thank you!
>
> Steven
>
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Re: [gmx-users] Regarding cosine content

[Tsjerk Wassenaar]

Hi Bipin,

It seems one of the proteins is taking longer to reach an equilibrium.
Maybe it is undergoing a conformational change?
Did you calculate the principal components per protein, or for the
joint trajectories? It would have been better to echo the commands you
used on the list, because it might result in a different
interpretation. I also made some comments on the list a short while
ago regarding the interpretation of projections and cosine content.
Maybe they can help you form a picture of what is happening :)

Hope it helps,

Tsjerk


On Thu, Nov 17, 2011 at 12:22 PM, bipin singh  wrote:
> Hello all,
>
> I have done PCA from 50ns long trajectory for two similar proteins
> (length 180 aa and RMSD 0.2 A).
> The equilibration time and final simulation condition were identical
> for both the protein.
> But when I checked the cosine content for PC1 for both proteins they
> were 0.9 and 0.5 respectively.
> What can be the reason for this huge difference in cosine content of
> the two proteins ?
>
>
> --
> ---
> Regards,
> Bipin Singh
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] Regarding cosine content

[bipin singh]

Thanks for the reply...
I calculated principal components per protein using the command
g_anaeig -f md.xtc -s md.tpr -v eigenvec.trr -eig eigenval.xvg -comp
eigcomp.xvg -rmsf eigrmsf.xvg -2d 2dproj.xvg -proj proj.xvg -tu ns
-extr extr.pdb -filt filt.xtc -first 1 -last 2

Also please suggest how one can differentiate between the two
scenarios, when the high cosine content is due to random diffusion or
conformational changes ?


On Thu, Nov 17, 2011 at 17:34, Tsjerk Wassenaar  wrote:
> Hi Bipin,
>
> It seems one of the proteins is taking longer to reach an equilibrium.
> Maybe it is undergoing a conformational change?
> Did you calculate the principal components per protein, or for the
> joint trajectories? It would have been better to echo the commands you
> used on the list, because it might result in a different
> interpretation. I also made some comments on the list a short while
> ago regarding the interpretation of projections and cosine content.
> Maybe they can help you form a picture of what is happening :)
>
> Hope it helps,
>
> Tsjerk
>
>
> On Thu, Nov 17, 2011 at 12:22 PM, bipin singh  wrote:
>> Hello all,
>>
>> I have done PCA from 50ns long trajectory for two similar proteins
>> (length 180 aa and RMSD 0.2 A).
>> The equilibration time and final simulation condition were identical
>> for both the protein.
>> But when I checked the cosine content for PC1 for both proteins they
>> were 0.9 and 0.5 respectively.
>> What can be the reason for this huge difference in cosine content of
>> the two proteins ?
>>
>>
>> --
>> ---
>> Regards,
>> Bipin Singh
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
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>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
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-- 
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Regards,
Bipin Singh
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[gmx-users] Cuda not detected

[Andrzej Rzepiela]

Hey,

I am playing with the gpu version of mdrun and could make it run with:

~/gromacs/gpu/bin/mdrun-gpu -s topol.tpr -device  
"OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes"


However after reboot of the machine ( which is a testing machine)

I get the following error:


---
Program mdrun-gpu, VERSION 4.5.5
Source code file: /home/weber/gromacs/gromacs-4.5.5_gpu/src/kernel/ 
openmm_wrapper.cpp, line: 1272


Fatal error:
The requested platform "Cuda" could not be found.


echo $LD_LIBRARY_PATH:/opt/software/ganglia-3.1.7/lib64:/opt/software/ 
htop-0.8.3:/usr/local/cuda/lib64:/usr/local/cuda/lib:/home/weber/ 
OpenMM3.1.1-Linux64/lib


echo $PATH/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/usr/games:/usr/ 
lib64/jvm/jre/bin:/opt/software/nvidia/3.2.16/cuda/bin:/opt/software/ 
ganglia-3.1.7/bin:/opt/software/htop-0.8.3/bin:/usr/lib/mit/bin:/usr/ 
lib/mit/sbin:.:/usr/local/cuda/bin:/home/weber/cmake-2.8.6/bin



I run a simple gpu test program and it  works.

I believe something is not linked correctly, maybe someone can give me  
a hint.


Thank You

Andrzej

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Re: [gmx-users] Regarding TIP4P structure

[Justin A. Lemkul]

Ravi Kumar Venkatraman wrote:

Dear all,
 Could anybody send me the link for getting the tip4p tip3p 
and tip5p single water structure in gro/pdb or in anyother format.




A single water molecule?  Copy and paste the coordinates from the existing .gro 
files in $GMXLIB.


-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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[gmx-users] Re: Umbrella Sampling - Justin tutorial

[Justin A. Lemkul]

Steven Neumann wrote:

Hi Justin,
 
I am sorry for so many questions but I do not understand something.
First we run the simulation of pulling Chain A from ChainB with constant 
force (pull_k1=1000) and constant velocity of pulling (pull_rate1=0.01) 
We extract windows as we discussed and then run simulations with those 
configurations as a starting point. I saw the trajectory of one of these 
simulations and it looks like normal MD simulation. My question is: Why 
do we have in mdp file still pull code as we do not pull protein chain 
any more? Pull rate is set to zero but force is still applied... why? Is 
this code just used to extract pullf.xvg and pullx.xvg which does not 
change too much?
I would appreciate the explanation as without undesratnding the basics 
its not good to do any simulation like this.
 


Have you read the WHAM paper, or the one specific for g_wham, or perhaps papers 
about umbrella sampling in general?  You should start there before diving in to 
doing the simulations.


The harmonic force applied in the SMD and US simulations is simply a biasing 
force to make something happen.  With a non-zero pull_rate, motion in a 
particular direction is forced to happen.  With a pull_rate of zero, the COM 
distance is simply restricted - the biasing force maintains the COM distance 
between the two defined species, while allowing it to oscillate according to a 
harmonic force defined by pull_k1.  Thus you establish sampling overlap between 
neighboring windows along the reaction coordinate.


-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] Cuda not detected

[Ye MEI]

try 
nvidia-smi -a
to see whether the GPU card has been correctly configured. 
This happens on my GPU node. Every time I reboot the computer, I must 
reconfigure the GPU cards with "nvidia-smi -a" using root account.

Ye
2011-11-17 



From： Andrzej Rzepiela 
Date： 2011-11-17  21:01:07 
To： gmx-users 
CC： 
Subject： [gmx-users] Cuda not detected 
 
Hey,
I am playing with the gpu version of mdrun and could make it run with:
~/gromacs/gpu/bin/mdrun-gpu -s topol.tpr -device  
"OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes"
However after reboot of the machine ( which is a testing machine)
I get the following error:
---
Program mdrun-gpu, VERSION 4.5.5
Source code file: /home/weber/gromacs/gromacs-4.5.5_gpu/src/kernel/ 
openmm_wrapper.cpp, line: 1272
Fatal error:
The requested platform "Cuda" could not be found.
echo $LD_LIBRARY_PATH:/opt/software/ganglia-3.1.7/lib64:/opt/software/ 
htop-0.8.3:/usr/local/cuda/lib64:/usr/local/cuda/lib:/home/weber/ 
OpenMM3.1.1-Linux64/lib
echo $PATH/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/usr/games:/usr/ 
lib64/jvm/jre/bin:/opt/software/nvidia/3.2.16/cuda/bin:/opt/software/ 
ganglia-3.1.7/bin:/opt/software/htop-0.8.3/bin:/usr/lib/mit/bin:/usr/ 
lib/mit/sbin:.:/usr/local/cuda/bin:/home/weber/cmake-2.8.6/bin
I run a simple gpu test program and it  works.
I believe something is not linked correctly, maybe someone can give me  
a hint.
Thank You
Andrzej
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[gmx-users] Gromacs 3D maps

[Alex]

Dear all,

I'd like to transform an md gromacs trajectory in a 3d maps set.
I mean that every 100ps, I need to export frame coordinates to a 3d map.
Than I need to compare a map with the following.
Could give me any advice about tools/software to use?

Additionally I need to export the coordinate (x,y,z) of atom's protein, deriving
from MD trajectory, to a matrix where each columns are frame number, 1-n
atoms'positions (x,y,z coordinates).
Any suggestion?

Thanks in advance

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Re: [gmx-users] Re: Umbrella Sampling - Justin tutorial

[Steven Neumann]

Thank you Justin, I will read it for sure and come back to my simulations!

Steven

On Thu, Nov 17, 2011 at 1:25 PM, Justin A. Lemkul  wrote:

>
>
> Steven Neumann wrote:
>
>> Hi Justin,
>>  I am sorry for so many questions but I do not understand something.
>> First we run the simulation of pulling Chain A from ChainB with constant
>> force (pull_k1=1000) and constant velocity of pulling (pull_rate1=0.01) We
>> extract windows as we discussed and then run simulations with those
>> configurations as a starting point. I saw the trajectory of one of these
>> simulations and it looks like normal MD simulation. My question is: Why do
>> we have in mdp file still pull code as we do not pull protein chain any
>> more? Pull rate is set to zero but force is still applied... why? Is this
>> code just used to extract pullf.xvg and pullx.xvg which does not change too
>> much?
>> I would appreciate the explanation as without undesratnding the basics
>> its not good to do any simulation like this.
>>
>>
>
> Have you read the WHAM paper, or the one specific for g_wham, or perhaps
> papers about umbrella sampling in general?  You should start there before
> diving in to doing the simulations.
>
> The harmonic force applied in the SMD and US simulations is simply a
> biasing force to make something happen.  With a non-zero pull_rate, motion
> in a particular direction is forced to happen.  With a pull_rate of zero,
> the COM distance is simply restricted - the biasing force maintains the COM
> distance between the two defined species, while allowing it to oscillate
> according to a harmonic force defined by pull_k1.  Thus you establish
> sampling overlap between neighboring windows along the reaction coordinate.
>
>
> -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
> 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] Cuda not detected

[Andrzej Rzepiela]

Hey,

thank you for the hint. I just finished the tests. The machine is   
Intel xeon R, 12 cores , 4 Teslas M2090  and 96 gb of memory.
I used the most demanding PME dhfr benchmark system ( 7000w + protein)  
and obtained the following results:


1 cpu core run: 2.135 ns a day
12 cpu cores run: 21.478 ns a day

1 gpu unit run ( how many cpu cores are used, one ? ):   13.0 ns/day

4  parallel gpu runs on the node,  performance:   12.884, 10.296,  
8.290 and  6.953 ns/day, which is on average about  9.6 ns for one gpu.


From your experience, are this expected numbers ? From the benchmarks  
on the website I had e feeling that the gpu runs will be faster.


Greetings

Andrzej





On Nov 17, 2011, at 2:26 PM, Ye MEI wrote:


try
nvidia-smi -a
to see whether the GPU card has been correctly configured.
This happens on my GPU node. Every time I reboot the computer, I  
must reconfigure the GPU cards with "nvidia-smi -a" using root  
account.


Ye
2011-11-17
From： Andrzej Rzepiela
Date： 2011-11-17  21:01:07
To： gmx-users
CC：
Subject： [gmx-users] Cuda not detected
Hey,
I am playing with the gpu version of mdrun and could make it run with:
~/gromacs/gpu/bin/mdrun-gpu -s topol.tpr -device
"OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes"
However after reboot of the machine ( which is a testing machine)
I get the following error:
---
Program mdrun-gpu, VERSION 4.5.5
Source code file: /home/weber/gromacs/gromacs-4.5.5_gpu/src/kernel/
openmm_wrapper.cpp, line: 1272
Fatal error:
The requested platform "Cuda" could not be found.
echo $LD_LIBRARY_PATH:/opt/software/ganglia-3.1.7/lib64:/opt/software/
htop-0.8.3:/usr/local/cuda/lib64:/usr/local/cuda/lib:/home/weber/
OpenMM3.1.1-Linux64/lib
echo $PATH/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/usr/games:/usr/
lib64/jvm/jre/bin:/opt/software/nvidia/3.2.16/cuda/bin:/opt/software/
ganglia-3.1.7/bin:/opt/software/htop-0.8.3/bin:/usr/lib/mit/bin:/usr/
lib/mit/sbin:.:/usr/local/cuda/bin:/home/weber/cmake-2.8.6/bin
I run a simple gpu test program and it  works.
I believe something is not linked correctly, maybe someone can give me
a hint.
Thank You
Andrzej
--
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[gmx-users] user contribution

[Thorsten Koeddermann]

Hallo all,

how can I upload a molecule topology? I registered as a user but when I
click at the attache file link "this page cannot be changed" appears. 

Thanks in advance for your help.

Thorsten  
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[gmx-users] calculate potential with tabulated non-bonded interactions

[Liu, Liang]

Dear all,

I am trying to calculate potentials for RNA structures with a serial of
tabulated potentials (non-bonded).
And the only potential I am going to use is the tabulated potentials, and
the effect from force field should be removed.
However, when I use pdb2gmx to build the topology file, I have to choose a
force field. What should I do for that? Thanks.

-- 
Best,
Liang Liu
-- 
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Re: [gmx-users] Cuda not detected

[Gianluca Santoni]

On 11/17/11 10:10 PM, Andrzej Rzepiela wrote:

Hey,

thank you for the hint. I just finished the tests. The machine 
is  Intel xeon R, 12 cores , 4 Teslas M2090  and 96 gb of memory.
I used the most demanding PME dhfr benchmark system ( 7000w + protein) 
and obtained the following results:


1 cpu core run: 2.135 ns a day
12 cpu cores run: 21.478 ns a day

1 gpu unit run ( how many cpu cores are used, one ? ):   13.0 ns/day

4  parallel gpu runs on the node,  performance:   12.884, 10.296, 
8.290 and  6.953 ns/day, which is on average about  9.6 ns for one gpu.


From your experience, are this expected numbers ? From the benchmarks 
on the website I had e feeling that the gpu runs will be faster.
GPU is faster with implicit solvent and other constraints up to now. 
They are optimizing everything for the next version of gromacs

http://www.gromacs.org/Developer_Zone/Roadmap/GROMACS_4.6

More detailed info on the gromacs manual.







--
Gianluca Santoni,
Institut de Biologie Structurale
41 rue Horowitz
Grenoble
_
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html

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Re: [gmx-users] calculate potential with tabulated non-bonded interactions

[Justin A. Lemkul]

Liu, Liang wrote:

Dear all,

I am trying to calculate potentials for RNA structures with a serial of 
tabulated potentials (non-bonded).
And the only potential I am going to use is the tabulated potentials, 
and the effect from force field should be removed.
However, when I use pdb2gmx to build the topology file, I have to choose 
a force field. What should I do for that? Thanks.




It sounds like you need to be constructing your own force field, completely, 
from scratch.  If you're not looking to use the existing force fields, this 
sounds like the only real solution.  You can take the time to make .xvg files 
for bonded and nonbonded interactions (see the manual), but that is probably 
just as much work and your simulations will be much slower.


-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] calculate potential with tabulated non-bonded interactions

[Liu, Liang]

Well, I already have the xvg files from others. However I don't know how to
use it.

On Thu, Nov 17, 2011 at 10:00 AM, Justin A. Lemkul  wrote:

>
>
> Liu, Liang wrote:
>
>> Dear all,
>>
>> I am trying to calculate potentials for RNA structures with a serial of
>> tabulated potentials (non-bonded).
>> And the only potential I am going to use is the tabulated potentials, and
>> the effect from force field should be removed.
>> However, when I use pdb2gmx to build the topology file, I have to choose
>> a force field. What should I do for that? Thanks.
>>
>>
> It sounds like you need to be constructing your own force field,
> completely, from scratch.  If you're not looking to use the existing force
> fields, this sounds like the only real solution.  You can take the time to
> make .xvg files for bonded and nonbonded interactions (see the manual), but
> that is probably just as much work and your simulations will be much slower.
>
> -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
> interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>



-- 
Best,
Liang Liu
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Re: [gmx-users] calculate potential with tabulated non-bonded interactions

[Justin A. Lemkul]

Liu, Liang wrote:
Well, I already have the xvg files from others. However I don't know how 
to use it.




Start with the manual, where modifications to the topology and relevant commands 
and files are described.  Then refer to the how-to online, which has specific 
instructions.  Then, ask specific questions of problems you are having.  I doubt 
anyone on this list will be able or willing to guess where your problems are at 
this point.


-Justin

On Thu, Nov 17, 2011 at 10:00 AM, Justin A. Lemkul > wrote:




Liu, Liang wrote:

Dear all,

I am trying to calculate potentials for RNA structures with a
serial of tabulated potentials (non-bonded).
And the only potential I am going to use is the tabulated
potentials, and the effect from force field should be removed.
However, when I use pdb2gmx to build the topology file, I have
to choose a force field. What should I do for that? Thanks.


It sounds like you need to be constructing your own force field,
completely, from scratch.  If you're not looking to use the existing
force fields, this sounds like the only real solution.  You can take
the time to make .xvg files for bonded and nonbonded interactions
(see the manual), but that is probably just as much work and your
simulations will be much slower.

-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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--
Best,
Liang Liu


--


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] user contribution

[Justin A. Lemkul]

Thorsten Koeddermann wrote:

Hallo all,

how can I upload a molecule topology? I registered as a user but when I
click at the attache file link "this page cannot be changed" appears. 


Thanks in advance for your help.


You have to email Rossen before you can modify anything.  His email is linked 
from the Gromacs homepage.


-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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[gmx-users] Hydrogen database

[Ehud Schreiber]

Hi,

I have recently studied the hydrogen database format of .hdb files (page
118, section 5.6.4 in the manual version 4.5.4). I would like to make a
few remarks that, if correct, may need addressing.

1)  Method 3 of adding the hydrogens, that of two planar hydrogens,
gives -NH2 as the example. I think this is misleading, as although this
is true for an amide group -C(=O)NH2 such as in an asparagine and
glutamine side chains, the nitrogen is tetrahedral in the R-NH2 case or
in the amino acid N-terminus. A better example for two planar hydrogens
would be =CH2 such as in ethylene or vinyls.  

2)  The provided methods for adding hydrogens are not covering the
whole set of possibilities. In particular, it seems to me that three
methods are lacking, although admittedly they are less common:

a.   One tetrahedral hydrogen connected to atom i which is in turn
connected to two atoms j,k such that n is on the plane bisecting angle
j-i-k; n-i-j = n-i-k = 109.47 degrees; and dihedral n-i-j-l > 90
degrees. Example: secondary amines R2NH. This case can be mimicked by
method 2 with i,j,l atoms so is perhaps superfluous.

b.  One planar hydrogen connected to atom i which is connected to
only one other atom j such that n-i-j = 120 degrees and n-i-j-k is
trans. Example: R2C=NH.

c.   One linear hydrogen such that n-i-j is a straight line.
Example: #CH where # is a triple bond.

3)  I haven't checked this, but can the k atom be a hydrogen added
in an earlier line of the same .hdb file?

What do you say?

Thanks,

Ehud Schreiber. 

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[gmx-users] Thanks Justin Lemkul

[Ravi Kumar Venkatraman]

*With Regards,
Ravi Kumar Venkatraman,
IPC Dept., IISc,
Bangalore, INDIA.

+91-9686933963.*
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[gmx-users] PMF with nanotube

[Vijayaraj]

Hello,

I am trying to find the PMF for the diffusion of small molecule through a
nanotube. I have generated the umbrella sampling windows from
pull_geometry=direction simulation and umbrella sampling with
pull_geometry=position. I guess the PMF for this system can be obtained by
combining the g_wham output of above and below of reference nanotube. I got
negative PMF curve for the above reference part and positive curve for the
below reference part. I should get a complete PMF curve when I combine the
above and below part. I dont understand why these two parts have different
signs.

Regards,
Vijay.
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[gmx-users] Re: gmx-users Digest, Vol 91, Issue 119

[Saba Ferdous]

gurations as a starting point. I saw the trajectory of one of these
> simulations and it looks like normal MD simulation. My question is: Why do
> we have in mdp file still pull code as we do not pull protein chain any
> more? Pull rate is set to zero but force is still applied... why? Is this
> code just used to extract pullf.xvg and pullx.xvg which does not change too
> much?
> I would appreciate the explanation as without undesratnding the basics its
> not good to do any simulation like this.
>
> Thank you
>
> Steven
>
>
>
>
> Are my questions to trivial or noones knows? Please, help!
>
> On Wed, Nov 16, 2011 at 9:31 AM, Steven Neumann  >wrote:
>
> > Hi GMX Users,
> >
> > I am doing Justin tutorial of Umbrella sampling. I have just finished
> > continous pulling of chainA from the reference chainB. I have some
> > questions. I looked at the trajectory of pulling and it has began with
> > dissociating residue 27Alanine from the ChainB following 26, 25, 24...1.
> My
> > question is why? As you apply pulling with the constant force to the COM
> of
> > the whole chain why does it start with terminal residue following then
> one
> > by one? Why not the middle one or any other?
> >
> > The second thing I would like to extract starting configurations from
> from
> > my pulling. Till frame 189 the COM varies from 0.49 to 0.56 - makes sense
> > as the ChainA is still within ChainB. I would like to use configurations:
> >
> > 0 - 0.50
> > 50 - 0.52
> > 100 - 0.51
> > 150 - 0.51
> > 200 - 0.62
> > 250 - 2.21
> > 
> > 500 - 5.48
> >
> > My question is: Do I have to use exactly the same e.g. 0.2 nm spacing or
> > this configuration above is ok? Can the spacing in nm vary?
> > And the last thing - is it required to use frames till 189 as the COM
> > varies in this area?
> >
> > Thank you!
> >
> > Steven
> >
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/2017/8b9ec4a6/attachment-0001.html
>
> --
>
> Message: 4
> Date: Thu, 17 Nov 2011 13:04:14 +0100
> From: Tsjerk Wassenaar 
> Subject: Re: [gmx-users] Regarding cosine content
> To: Discussion list for GROMACS users 
> Message-ID:
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Bipin,
>
> It seems one of the proteins is taking longer to reach an equilibrium.
> Maybe it is undergoing a conformational change?
> Did you calculate the principal components per protein, or for the
> joint trajectories? It would have been better to echo the commands you
> used on the list, because it might result in a different
> interpretation. I also made some comments on the list a short while
> ago regarding the interpretation of projections and cosine content.
> Maybe they can help you form a picture of what is happening :)
>
> Hope it helps,
>
> Tsjerk
>
>
> On Thu, Nov 17, 2011 at 12:22 PM, bipin singh 
> wrote:
> > Hello all,
> >
> > I have done PCA from 50ns long trajectory for two similar proteins
> > (length 180 aa and RMSD 0.2 A).
> > The equilibration time and final simulation condition were identical
> > for both the protein.
> > But when I checked the cosine content for PC1 for both proteins they
> > were 0.9 and 0.5 respectively.
> > What can be the reason for this huge difference in cosine content of
> > the two proteins ?
> >
> >
> > --
> > ---
> > Regards,
> > Bipin Singh
> > --
> > 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
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
>
>
> --
>
> Message: 5
> Date: Thu, 17 Nov 2011 18:07:44 +0530
> From: bipin singh 
> Subject: Re: [gmx-users] Regarding cosine content
> To: Discussion list for GROMACS users 
> Message-ID:
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> 

Re: [gmx-users] calculate potential with tabulated non-bonded interactions

[Liu, Liang]

Well my first question is: if the pdb2gmx command must take a force file? I
guess it should be necessary. Then the available list contains amber and
others, but not user-specified potential. This will affect the future
simulation or calculation?

On Thu, Nov 17, 2011 at 10:06 AM, Justin A. Lemkul  wrote:

>
>
> Liu, Liang wrote:
>
>> Well, I already have the xvg files from others. However I don't know how
>> to use it.
>>
>>
> Start with the manual, where modifications to the topology and relevant
> commands and files are described.  Then refer to the how-to online, which
> has specific instructions.  Then, ask specific questions of problems you
> are having.  I doubt anyone on this list will be able or willing to guess
> where your problems are at this point.
>
> -Justin
>
>  On Thu, Nov 17, 2011 at 10:00 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Liu, Liang wrote:
>>
>>Dear all,
>>
>>I am trying to calculate potentials for RNA structures with a
>>serial of tabulated potentials (non-bonded).
>>And the only potential I am going to use is the tabulated
>>potentials, and the effect from force field should be removed.
>>However, when I use pdb2gmx to build the topology file, I have
>>to choose a force field. What should I do for that? Thanks.
>>
>>
>>It sounds like you need to be constructing your own force field,
>>completely, from scratch.  If you're not looking to use the existing
>>force fields, this sounds like the only real solution.  You can take
>>the time to make .xvg files for bonded and nonbonded interactions
>>(see the manual), but that is probably just as much work and your
>>simulations will be much slower.
>>
>>-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/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
>>
>>
>> 
>> >
>>
>>
>>
>>
>> --
>> Best,
>> Liang Liu
>>
>
> --
> ==**==
>
> 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!
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> interface or send it to gmx-users-requ...@gromacs.org.
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>



-- 
Best,
Liang Liu
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Re: [gmx-users] GROMACS/ORCA QMMM

[Jose Tusell]

Hi Cristoph,

Thanks for the reply.  I found that my problem was not gromacs.  The
input that ORCA was receiving from GROMACS did not have the correct
number of hydrogens.  I've solved this problem now and ORCA is running
fine.  I however ran into another problem with my energy minimization.
 The output from my gromacs log file is the following:

   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
   Bond  AngleProper Dih.  Improper Dih.  LJ-14
1.21899e+041.92496e+035.62567e+031.49141e+013.68001e+03
 Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.Quantum En.
2.41200e+041.47494e+05   -5.06544e+05   -7.56009e+04   -3.96508e+06
  Potential Pressure (bar)
   -4.35218e+06   -2.10629e+04

   Step   Time Lambda
  11.00.0

   Energies (kJ/mol)
   Bond  AngleProper Dih.  Improper Dih.  LJ-14
1.20006e+041.92297e+035.62600e+031.47801e+013.67746e+03
 Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.Quantum En.
2.41174e+041.46421e+05   -5.06609e+05   -7.56156e+04   -4.00402e+06
  Potential Pressure (bar)
   -4.39246e+06   -2.10739e+04

   Step   Time Lambda
  22.00.0

   Energies (kJ/mol)
   Bond  AngleProper Dih.  Improper Dih.  LJ-14
1.17961e+041.92126e+035.62633e+031.46477e+013.67461e+03
 Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.Quantum En.
2.41145e+041.45528e+05   -5.06679e+05   -7.56315e+04   -4.18671e+06
  Potential Pressure (bar)
   -4.57635e+06   -2.10854e+04

   Step   Time Lambda
  33.00.0

   Step   Time Lambda
  44.00.0

   Energies (kJ/mol)
   Bond  AngleProper Dih.  Improper Dih.  LJ-14
1.16705e+041.92041e+035.62652e+031.45728e+013.67282e+03
 Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.Quantum En.
2.41128e+041.45113e+05   -5.06721e+05   -7.56410e+04   -4.24486e+06
  Potential Pressure (bar)
   -4.63509e+06   -2.10913e+04

   Step   Time Lambda
  55.00.0

   Step   Time Lambda
  66.00.0

   Step   Time Lambda
  77.00.0

   Step   Time Lambda
  88.00.0

   Step   Time Lambda
  99.00.0

   Step   Time Lambda
 10   10.00.0

   Step   Time Lambda
 11   11.00.0

   Step   Time Lambda
 12   12.00.0

   Step   Time Lambda
 13   13.00.0

   Step   Time Lambda
 14   14.00.0

   Step   Time Lambda
 15   15.00.0

   Step   Time Lambda
 16   16.00.0

   Step   Time Lambda
 17   17.00.0

   Step   Time Lambda
 18   18.00.0


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.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

Why doesn't GROMACS output the energies for certain steps?  Step 3 and
steps 5-18 do show any output in the log file.  Any ideas why this is
happening?

Thanks,

Jose Tusell
On Mon, Nov 14, 2011 at 7:05 AM, Christoph Riplinger
 wrote:
> Dear Jose,
>
> I tried oniom which stopped for me either (although without a segfault).
> Have you tried "QMMMscheme normal"?
>
> Christoph
>
> On 11/11/2011 05:53 PM, Jose Tusell wrote:
>>
>> Dear GROMACS users,
>>
>> I'm trying to run a QM-MM optimization.  I solvate my protein and add
>> ions then I do a classical optimization (just GROMACS).  After that I
>> run grompp with the following minim.mdp file (just showing qmmm
>> options):
>>
>> QMMM            = yes
>> QMMM-grps       = Other
>> QMmethod        = RHF
>> QMbasis         = 3-21G
>> QMMMscheme      = Oniom
>> QMcharge        = -1
>> QMmult          = 1
>> SH              = no
>>
>> This creates the *.tpr file that use to run mdrun.  I use the
>> following *.ORCAINFO file:
>>
>> !PAL8 Quick-DFT VerySlowConv
>> %scf
>

Re: [gmx-users] Strange problem.complex out of Box after EM

[Justin A. Lemkul]

Please change the subject line to the relevant topic and do not paste the entire 
digest.  I guess the archive is already somewhat hopeless, but let's not make it 
worse :)


Saba Ferdous wrote:

Dear Justin,

I have set 1.5 dodecahedron. i centered the complex in box.
complex.gro, complexsol.gro and complex_sol_ions.gro seems inside in 
box. I m using VMD for visualization. i have rotated it in 3D
while when after EM step, i visualize em.gro then half complex seems 
outside the box. is there any way to center em.gro after energy 
minimization?




Again, this is just a matter of visualization.  There is nothing wrong and 
nothing needed to fix.  You can rewrap the periodic cell with


trjconv -pbc mol -ur compact

if you find you want more convenient visualization.

-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] calculate potential with tabulated non-bonded interactions

[Justin A. Lemkul]

Liu, Liang wrote:
Well my first question is: if the pdb2gmx command must take a force 
file? I guess it should be necessary. Then the available list contains 
amber and others, but not user-specified potential. This will affect the 
future simulation or calculation?




Yes.  Gromacs allows you provide tabulated potentials for van der Waals and 
Coulombic interactions (nonbonded), as well as bonded terms.  The complication 
is that force fields are somewhat more complex than that.  For instance, there 
are intramolecular terms (such as 1-4 interactions) that may or may not be 
scaled, depending on the force field used.


If you have a completely custom force field and you are trying to override all 
elements of an existing force field, it is better to simply write a new force 
field rather than attempt to hack an old one.


-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] GROMACS/ORCA QMMM

[Justin A. Lemkul]

Jose Tusell wrote:

Hi Cristoph,

Thanks for the reply.  I found that my problem was not gromacs.  The
input that ORCA was receiving from GROMACS did not have the correct
number of hydrogens.  I've solved this problem now and ORCA is running
fine.  I however ran into another problem with my energy minimization.
 The output from my gromacs log file is the following:

   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
   Bond  AngleProper Dih.  Improper Dih.  LJ-14
1.21899e+041.92496e+035.62567e+031.49141e+013.68001e+03
 Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.Quantum En.
2.41200e+041.47494e+05   -5.06544e+05   -7.56009e+04   -3.96508e+06
  Potential Pressure (bar)
   -4.35218e+06   -2.10629e+04

   Step   Time Lambda
  11.00.0

   Energies (kJ/mol)
   Bond  AngleProper Dih.  Improper Dih.  LJ-14
1.20006e+041.92297e+035.62600e+031.47801e+013.67746e+03
 Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.Quantum En.
2.41174e+041.46421e+05   -5.06609e+05   -7.56156e+04   -4.00402e+06
  Potential Pressure (bar)
   -4.39246e+06   -2.10739e+04

   Step   Time Lambda
  22.00.0

   Energies (kJ/mol)
   Bond  AngleProper Dih.  Improper Dih.  LJ-14
1.17961e+041.92126e+035.62633e+031.46477e+013.67461e+03
 Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.Quantum En.
2.41145e+041.45528e+05   -5.06679e+05   -7.56315e+04   -4.18671e+06
  Potential Pressure (bar)
   -4.57635e+06   -2.10854e+04

   Step   Time Lambda
  33.00.0

   Step   Time Lambda
  44.00.0

   Energies (kJ/mol)
   Bond  AngleProper Dih.  Improper Dih.  LJ-14
1.16705e+041.92041e+035.62652e+031.45728e+013.67282e+03
 Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.Quantum En.
2.41128e+041.45113e+05   -5.06721e+05   -7.56410e+04   -4.24486e+06
  Potential Pressure (bar)
   -4.63509e+06   -2.10913e+04

   Step   Time Lambda
  55.00.0

   Step   Time Lambda
  66.00.0

   Step   Time Lambda
  77.00.0

   Step   Time Lambda
  88.00.0

   Step   Time Lambda
  99.00.0

   Step   Time Lambda
 10   10.00.0

   Step   Time Lambda
 11   11.00.0

   Step   Time Lambda
 12   12.00.0

   Step   Time Lambda
 13   13.00.0

   Step   Time Lambda
 14   14.00.0

   Step   Time Lambda
 15   15.00.0

   Step   Time Lambda
 16   16.00.0

   Step   Time Lambda
 17   17.00.0

   Step   Time Lambda
 18   18.00.0


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.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

Why doesn't GROMACS output the energies for certain steps?  Step 3 and
steps 5-18 do show any output in the log file.  Any ideas why this is
happening?



This happens for the reasons printed by mdrun - those steps caused no change in 
energy.


-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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[gmx-users] Regarding Shell Molecular Dynamics

[Ravi Kumar Venkatraman]

Dear All,
 Is it not possible to minimize using cg with flexible
constraints?

Thank you In advance.

*With Regards,
Ravi Kumar Venkatraman,
IPC Dept., IISc,
Bangalore, INDIA.

+91-9686933963.*
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Re: [gmx-users] GROMACS/ORCA QMMM

[Jose Tusell]

Hi Justin,

Thanks for the input on why this is happening.   It sounds a little
suspicious that the energy doesn't change after a few steps of energy
minimization.  Do you know of any way that I can find out what is
going on?

Thanks,

Jose Tusell

On Thu, Nov 17, 2011 at 10:58 AM, Justin A. Lemkul  wrote:
>
>
> Jose Tusell wrote:
>>
>> Hi Cristoph,
>>
>> Thanks for the reply.  I found that my problem was not gromacs.  The
>> input that ORCA was receiving from GROMACS did not have the correct
>> number of hydrogens.  I've solved this problem now and ORCA is running
>> fine.  I however ran into another problem with my energy minimization.
>>  The output from my gromacs log file is the following:
>>
>>           Step           Time         Lambda
>>              0        0.0        0.0
>>
>>   Energies (kJ/mol)
>>           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
>>    1.21899e+04    1.92496e+03    5.62567e+03    1.49141e+01    3.68001e+03
>>     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.    Quantum En.
>>    2.41200e+04    1.47494e+05   -5.06544e+05   -7.56009e+04   -3.96508e+06
>>      Potential Pressure (bar)
>>   -4.35218e+06   -2.10629e+04
>>
>>           Step           Time         Lambda
>>              1        1.0        0.0
>>
>>   Energies (kJ/mol)
>>           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
>>    1.20006e+04    1.92297e+03    5.62600e+03    1.47801e+01    3.67746e+03
>>     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.    Quantum En.
>>    2.41174e+04    1.46421e+05   -5.06609e+05   -7.56156e+04   -4.00402e+06
>>      Potential Pressure (bar)
>>   -4.39246e+06   -2.10739e+04
>>
>>           Step           Time         Lambda
>>              2        2.0        0.0
>>
>>   Energies (kJ/mol)
>>           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
>>    1.17961e+04    1.92126e+03    5.62633e+03    1.46477e+01    3.67461e+03
>>     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.    Quantum En.
>>    2.41145e+04    1.45528e+05   -5.06679e+05   -7.56315e+04   -4.18671e+06
>>      Potential Pressure (bar)
>>   -4.57635e+06   -2.10854e+04
>>
>>           Step           Time         Lambda
>>              3        3.0        0.0
>>
>>           Step           Time         Lambda
>>              4        4.0        0.0
>>
>>   Energies (kJ/mol)
>>           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
>>    1.16705e+04    1.92041e+03    5.62652e+03    1.45728e+01    3.67282e+03
>>     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.    Quantum En.
>>    2.41128e+04    1.45113e+05   -5.06721e+05   -7.56410e+04   -4.24486e+06
>>      Potential Pressure (bar)
>>   -4.63509e+06   -2.10913e+04
>>
>>           Step           Time         Lambda
>>              5        5.0        0.0
>>
>>           Step           Time         Lambda
>>              6        6.0        0.0
>>
>>           Step           Time         Lambda
>>              7        7.0        0.0
>>
>>           Step           Time         Lambda
>>              8        8.0        0.0
>>
>>           Step           Time         Lambda
>>              9        9.0        0.0
>>
>>           Step           Time         Lambda
>>             10       10.0        0.0
>>
>>           Step           Time         Lambda
>>             11       11.0        0.0
>>
>>           Step           Time         Lambda
>>             12       12.0        0.0
>>
>>           Step           Time         Lambda
>>             13       13.0        0.0
>>
>>           Step           Time         Lambda
>>             14       14.0        0.0
>>
>>           Step           Time         Lambda
>>             15       15.0        0.0
>>
>>           Step           Time         Lambda
>>             16       16.0        0.0
>>
>>           Step           Time         Lambda
>>             17       17.0        0.0
>>
>>           Step           Time         Lambda
>>             18       18.0        0.0
>>
>>
>> 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.
>> You might need to increase your constraint accuracy, or turn
>> off constraints alltogether (set constraints = none in mdp file)
>>
>> Why doesn't GROMACS output the energies for certain steps?  Step 3 and
>> steps 5-18 do show any output in the log file.  Any ideas why this is
>> happening?
>>
>
> This happens for the reasons printed by mdrun - those steps caused no change
> in energy.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, V

Re: [gmx-users] GROMACS/ORCA QMMM

[Justin A. Lemkul]

Jose Tusell wrote:

Hi Justin,

Thanks for the input on why this is happening.   It sounds a little
suspicious that the energy doesn't change after a few steps of energy
minimization.  Do you know of any way that I can find out what is
going on?



The screen output should indicate the atom with maximal force.  Sometimes the EM 
algorithms get stuck when the geometry cannot change without making detrimental 
moves.  You either need a larger step size, a different algorithm, or a better 
starting structure, if that is the case.  I have seen this many times before, 
nothing suspicious about it.


-Justin


Thanks,

Jose Tusell

On Thu, Nov 17, 2011 at 10:58 AM, Justin A. Lemkul  wrote:


Jose Tusell wrote:

Hi Cristoph,

Thanks for the reply.  I found that my problem was not gromacs.  The
input that ORCA was receiving from GROMACS did not have the correct
number of hydrogens.  I've solved this problem now and ORCA is running
fine.  I however ran into another problem with my energy minimization.
 The output from my gromacs log file is the following:

  Step   Time Lambda
 00.00.0

  Energies (kJ/mol)
  Bond  AngleProper Dih.  Improper Dih.  LJ-14
   1.21899e+041.92496e+035.62567e+031.49141e+013.68001e+03
Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.Quantum En.
   2.41200e+041.47494e+05   -5.06544e+05   -7.56009e+04   -3.96508e+06
 Potential Pressure (bar)
  -4.35218e+06   -2.10629e+04

  Step   Time Lambda
 11.00.0

  Energies (kJ/mol)
  Bond  AngleProper Dih.  Improper Dih.  LJ-14
   1.20006e+041.92297e+035.62600e+031.47801e+013.67746e+03
Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.Quantum En.
   2.41174e+041.46421e+05   -5.06609e+05   -7.56156e+04   -4.00402e+06
 Potential Pressure (bar)
  -4.39246e+06   -2.10739e+04

  Step   Time Lambda
 22.00.0

  Energies (kJ/mol)
  Bond  AngleProper Dih.  Improper Dih.  LJ-14
   1.17961e+041.92126e+035.62633e+031.46477e+013.67461e+03
Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.Quantum En.
   2.41145e+041.45528e+05   -5.06679e+05   -7.56315e+04   -4.18671e+06
 Potential Pressure (bar)
  -4.57635e+06   -2.10854e+04

  Step   Time Lambda
 33.00.0

  Step   Time Lambda
 44.00.0

  Energies (kJ/mol)
  Bond  AngleProper Dih.  Improper Dih.  LJ-14
   1.16705e+041.92041e+035.62652e+031.45728e+013.67282e+03
Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.Quantum En.
   2.41128e+041.45113e+05   -5.06721e+05   -7.56410e+04   -4.24486e+06
 Potential Pressure (bar)
  -4.63509e+06   -2.10913e+04

  Step   Time Lambda
 55.00.0

  Step   Time Lambda
 66.00.0

  Step   Time Lambda
 77.00.0

  Step   Time Lambda
 88.00.0

  Step   Time Lambda
 99.00.0

  Step   Time Lambda
10   10.00.0

  Step   Time Lambda
11   11.00.0

  Step   Time Lambda
12   12.00.0

  Step   Time Lambda
13   13.00.0

  Step   Time Lambda
14   14.00.0

  Step   Time Lambda
15   15.00.0

  Step   Time Lambda
16   16.00.0

  Step   Time Lambda
17   17.00.0

  Step   Time Lambda
18   18.00.0


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.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

Why doesn't GROMACS output the energies for certain steps?  Step 3 and
steps 5-18 do show any output in the log file.  Any ideas why this is
happening?


This happens for the reasons printed by mdrun - those steps caused no change
in energy.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
D

[gmx-users] what's the math algorithm?

[Liu, Liang]

Dear all,

Assuming I have a some tabulated potentials, table.xvg, tablep.xvg,
table_P_P.xvg, table_P_C.xvg and so on.
Also there are non-zero values in the first column of both table.xvg and
tablep.xvg; while the first column (x), the six column (h(x)) and the last
column (h'(x)) have non-zero numbers.
All other columns have only 0. So what's the math behind it? Thanks.

-- 
Best,
Liang Liu
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Re: [gmx-users] query for energy minimization in solvent

[Anushree Tripathi]

Yes I m using 4.0.7 version.so for that how could I change the name
accordingly.

On Sat, Nov 5, 2011 at 1:37 AM, Justin A. Lemkul  wrote:

>
>
> Anushree Tripathi wrote:
>
>> when i run the given command i.e,
>>
>> grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr
>> It is showing fatal error:No such molecule type NA.
>> How could I troubleshoot this problem?
>>
>>
> Ion naming is listed in ions.itp - the "NA" name works for all force
> fields in the Gromacs 4.5.x series.  Older versions had force
> field-specific naming so you will have to change the name accordingly if
> you're using one of these versions.
>
> -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
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> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
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Re: [gmx-users] GROMACS/ORCA QMMM

[Jose Tusell]

I'll try changing the step size first and if that fails I'll try
another algorithm.  Thanks for the input.

Jose Tusell

On Thu, Nov 17, 2011 at 11:48 AM, Justin A. Lemkul  wrote:
>
>
> Jose Tusell wrote:
>>
>> Hi Justin,
>>
>> Thanks for the input on why this is happening.   It sounds a little
>> suspicious that the energy doesn't change after a few steps of energy
>> minimization.  Do you know of any way that I can find out what is
>> going on?
>>
>
> The screen output should indicate the atom with maximal force.  Sometimes
> the EM algorithms get stuck when the geometry cannot change without making
> detrimental moves.  You either need a larger step size, a different
> algorithm, or a better starting structure, if that is the case.  I have seen
> this many times before, nothing suspicious about it.
>
> -Justin
>
>> Thanks,
>>
>> Jose Tusell
>>
>> On Thu, Nov 17, 2011 at 10:58 AM, Justin A. Lemkul 
>> wrote:
>>>
>>> Jose Tusell wrote:

 Hi Cristoph,

 Thanks for the reply.  I found that my problem was not gromacs.  The
 input that ORCA was receiving from GROMACS did not have the correct
 number of hydrogens.  I've solved this problem now and ORCA is running
 fine.  I however ran into another problem with my energy minimization.
  The output from my gromacs log file is the following:

          Step           Time         Lambda
             0        0.0        0.0

  Energies (kJ/mol)
          Bond          Angle    Proper Dih.  Improper Dih.
  LJ-14
   1.21899e+04    1.92496e+03    5.62567e+03    1.49141e+01
  3.68001e+03
    Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.    Quantum
 En.
   2.41200e+04    1.47494e+05   -5.06544e+05   -7.56009e+04
 -3.96508e+06
     Potential Pressure (bar)
  -4.35218e+06   -2.10629e+04

          Step           Time         Lambda
             1        1.0        0.0

  Energies (kJ/mol)
          Bond          Angle    Proper Dih.  Improper Dih.
  LJ-14
   1.20006e+04    1.92297e+03    5.62600e+03    1.47801e+01
  3.67746e+03
    Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.    Quantum
 En.
   2.41174e+04    1.46421e+05   -5.06609e+05   -7.56156e+04
 -4.00402e+06
     Potential Pressure (bar)
  -4.39246e+06   -2.10739e+04

          Step           Time         Lambda
             2        2.0        0.0

  Energies (kJ/mol)
          Bond          Angle    Proper Dih.  Improper Dih.
  LJ-14
   1.17961e+04    1.92126e+03    5.62633e+03    1.46477e+01
  3.67461e+03
    Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.    Quantum
 En.
   2.41145e+04    1.45528e+05   -5.06679e+05   -7.56315e+04
 -4.18671e+06
     Potential Pressure (bar)
  -4.57635e+06   -2.10854e+04

          Step           Time         Lambda
             3        3.0        0.0

          Step           Time         Lambda
             4        4.0        0.0

  Energies (kJ/mol)
          Bond          Angle    Proper Dih.  Improper Dih.
  LJ-14
   1.16705e+04    1.92041e+03    5.62652e+03    1.45728e+01
  3.67282e+03
    Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.    Quantum
 En.
   2.41128e+04    1.45113e+05   -5.06721e+05   -7.56410e+04
 -4.24486e+06
     Potential Pressure (bar)
  -4.63509e+06   -2.10913e+04

          Step           Time         Lambda
             5        5.0        0.0

          Step           Time         Lambda
             6        6.0        0.0

          Step           Time         Lambda
             7        7.0        0.0

          Step           Time         Lambda
             8        8.0        0.0

          Step           Time         Lambda
             9        9.0        0.0

          Step           Time         Lambda
            10       10.0        0.0

          Step           Time         Lambda
            11       11.0        0.0

          Step           Time         Lambda
            12       12.0        0.0

          Step           Time         Lambda
            13       13.0        0.0

          Step           Time         Lambda
            14       14.0        0.0

          Step           Time         Lambda
            15       15.0        0.0

          Step           Time         Lambda
            16       16.0        0.0

          Step           Time         Lambda
            17       17.0        0.0

          Step           Time         Lambda
            18       18.0        0.0


 Steps

Re: [gmx-users] GROMACS/ORCA QMMM

[swati patel]

hello,
I am trying to simulate streptavidin tetramer-biotin complex.I ve
calculated Ligand topology from a sofware PRODRG using gromos87 force
fields.After solvating it,I am getting an error using grompp command

Fatal error:
Atomtype HW not found

can anyone provide me some help?

Thanx with anticipation.


On Fri, Nov 18, 2011 at 2:29 AM, Jose Tusell  wrote:

> I'll try changing the step size first and if that fails I'll try
> another algorithm.  Thanks for the input.
>
> Jose Tusell
>
> On Thu, Nov 17, 2011 at 11:48 AM, Justin A. Lemkul 
> wrote:
> >
> >
> > Jose Tusell wrote:
> >>
> >> Hi Justin,
> >>
> >> Thanks for the input on why this is happening.   It sounds a little
> >> suspicious that the energy doesn't change after a few steps of energy
> >> minimization.  Do you know of any way that I can find out what is
> >> going on?
> >>
> >
> > The screen output should indicate the atom with maximal force.  Sometimes
> > the EM algorithms get stuck when the geometry cannot change without
> making
> > detrimental moves.  You either need a larger step size, a different
> > algorithm, or a better starting structure, if that is the case.  I have
> seen
> > this many times before, nothing suspicious about it.
> >
> > -Justin
> >
> >> Thanks,
> >>
> >> Jose Tusell
> >>
> >> On Thu, Nov 17, 2011 at 10:58 AM, Justin A. Lemkul 
> >> wrote:
> >>>
> >>> Jose Tusell wrote:
> 
>  Hi Cristoph,
> 
>  Thanks for the reply.  I found that my problem was not gromacs.  The
>  input that ORCA was receiving from GROMACS did not have the correct
>  number of hydrogens.  I've solved this problem now and ORCA is running
>  fine.  I however ran into another problem with my energy minimization.
>   The output from my gromacs log file is the following:
> 
>   Step   Time Lambda
>  00.00.0
> 
>   Energies (kJ/mol)
>   Bond  AngleProper Dih.  Improper Dih.
>   LJ-14
>    1.21899e+041.92496e+035.62567e+031.49141e+01
>   3.68001e+03
> Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.Quantum
>  En.
>    2.41200e+041.47494e+05   -5.06544e+05   -7.56009e+04
>  -3.96508e+06
>  Potential Pressure (bar)
>   -4.35218e+06   -2.10629e+04
> 
>   Step   Time Lambda
>  11.00.0
> 
>   Energies (kJ/mol)
>   Bond  AngleProper Dih.  Improper Dih.
>   LJ-14
>    1.20006e+041.92297e+035.62600e+031.47801e+01
>   3.67746e+03
> Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.Quantum
>  En.
>    2.41174e+041.46421e+05   -5.06609e+05   -7.56156e+04
>  -4.00402e+06
>  Potential Pressure (bar)
>   -4.39246e+06   -2.10739e+04
> 
>   Step   Time Lambda
>  22.00.0
> 
>   Energies (kJ/mol)
>   Bond  AngleProper Dih.  Improper Dih.
>   LJ-14
>    1.17961e+041.92126e+035.62633e+031.46477e+01
>   3.67461e+03
> Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.Quantum
>  En.
>    2.41145e+041.45528e+05   -5.06679e+05   -7.56315e+04
>  -4.18671e+06
>  Potential Pressure (bar)
>   -4.57635e+06   -2.10854e+04
> 
>   Step   Time Lambda
>  33.00.0
> 
>   Step   Time Lambda
>  44.00.0
> 
>   Energies (kJ/mol)
>   Bond  AngleProper Dih.  Improper Dih.
>   LJ-14
>    1.16705e+041.92041e+035.62652e+031.45728e+01
>   3.67282e+03
> Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.Quantum
>  En.
>    2.41128e+041.45113e+05   -5.06721e+05   -7.56410e+04
>  -4.24486e+06
>  Potential Pressure (bar)
>   -4.63509e+06   -2.10913e+04
> 
>   Step   Time Lambda
>  55.00.0
> 
>   Step   Time Lambda
>  66.00.0
> 
>   Step   Time Lambda
>  77.00.0
> 
>   Step   Time Lambda
>  88.00.0
> 
>   Step   Time Lambda
>  99.00.0
> 
>   Step   Time Lambda
> 10   10.00.0
> 
>   Step   Time Lambda
> 11   11.00.0
> 
>   Step   Time Lambda
> 12   12.00.0
> 
> >>>

[gmx-users] non-specific protein-protein interactions

[Ben Reynwar]

Dear gromacs list,

Does anyone know how well current force fields capture the energetics
of non-specific protein-protein interactions?  I'm simulating a
protein with an arm that alternates between (apparently) non-specific
adsorption to the main-body of the protein and free movement in the
solvent.  Can I place any trust in the results of an MD simulation for
something like this?  I haven't seen any comparison of experimental
results with simulation results of the energetics of non-specific
protein-protein interactions so I'm a little skeptical about it.
Currently I'm using generalized born implicit solvent, which is
perhaps a mistake when solvation energies could be critical to the
results.

Cheers,
Ben
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Re: [gmx-users] query for energy minimization in solvent

[Justin A. Lemkul]

Anushree Tripathi wrote:
Yes I m using 4.0.7 version.so for that how could I change the name 
accordingly.




Check ions.itp and use the names required by your chosen force field.

-Justin

On Sat, Nov 5, 2011 at 1:37 AM, Justin A. Lemkul > wrote:




Anushree Tripathi wrote:

when i run the given command i.e,

grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr
It is showing fatal error:No such molecule type NA.
How could I troubleshoot this problem?


Ion naming is listed in ions.itp - the "NA" name works for all force
fields in the Gromacs 4.5.x series.  Older versions had force
field-specific naming so you will have to change the name
accordingly if you're using one of these versions.

-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
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Virginia Tech
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[gmx-users] Poor exchange probability for REMD

[ÏéÇ« ¿×]

Dear GMX users，
   Recently i am performing the REMD simulation with Gromacs program and the 
temperature distribution for each replica was predicted with the server 
"http://folding.bmc.uu.se/remd/";. However, after a 2-ns short test simulation 
with 64 replicas  , i checked the exchange probability for the neighboring 
replicas and find the exchange probability was about 0.3 to 0.4 (as the file i 
attached )but the desired probability was 0.2. Meanwhile, i found the exchange 
probabilities fluctuated markedly for each pair of  replicas while ideally we 
may hope they were consistent with each other.  I don't know whether this is 
acceptable or must be fixed up, or  a longer simulation time and 
pre-equilibrium at different replica temperature for each replica was needed. 
The system i simulated  includes 60074 atoms which consists of 155 
residues,19173 waters and 14 chloridions. I first equilibrium the system for 
2ns with NPT ensemble at 300K, then start the REMD simulation for 64 different 
replicas (temperature ranges from 300 to 386K) with NVT ensemble and the 
exchange attempt time was 2-ps(1000 integral steps).   
Now i was totally puzzled and don't know how to figure out these problems,i 
am eager for the help from you and any suggestions will be greatly appreciated!
Best regards! 
Xiangqian Kong
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Re: [gmx-users] Hydrogen database

[Peter C. Lai]

Most of the issues should wash out after energy minimization anyway, so
I wouldn't care about bond angles too much. Just remember: the topology 
controls the geometry not the hydrogen database. Yes the hdb file format 
isn't too intuitive but after awhile I figured it out. Here some examples 
of hydrogens connected to SP and SP3 hybridized heavy atoms.

I parameterize saturated hydrocarbon backbones a lot, so here is an example 
of 1-heptanol (HPOH):

Atom Assignments (from the rtp entry):

  H72H31  H21  H12
   |  ||   |
 H71--C7--..--C3--C2--C1-H11
   |  ||   |
  H73H32  H22  O1-HO1

HDB entry:
HPOH 8
1 2 HO1 O1 C1 H11
2 6 H1 C1 C2 O1
2 6 H2 C2 C3 C1
2 6 H3 C3 C4 C2
2 6 H4 C4 C5 C3
2 6 H5 C5 C6 C4
2 6 H6 C6 C7 C5
3 4 H7 C7 C1 O1

Here is isopentyl acetate (isoamyl acetate) (3-methyl-1-butyl-ethanoate) 
(IPAC):
Atom Assignments (from the rtp entry):

  H12
  |
  H11-C1-H13
  | 
  C=O
  /
 OM
  \
  H21-C2-H22
  |
  H31-C3-H32
  | 
  C4-H41
 / \
/   \
 H411-C41   C42-H423
 /  |   |  \
 H412 H413 H421 H422

HDB entry:
IPAC 6
3 4 H1 C1 C O
2 6 H2 C2 C3 OM
2 6 H3 C3 C4 C2
1 2 H41 C4 C41 C3
3 4 H41 C41 C4 C3
3 4 H42 C42 C4 C3


On 2011-11-17 10:11:52AM -0600, Ehud Schreiber wrote:
> Hi,
> I have recently studied the hydrogen database format of .hdb files (page 118, 
> section 5.6.4 in the manual version 4.5.4). I would like to make a few 
> remarks that, if correct, may need addressing.
> 
> 1)  Method 3 of adding the hydrogens, that of two planar hydrogens, gives 
> -NH2 as the example. I think this is misleading, as although this is true for 
> an amide group –C(=O)NH2 such as in an asparagine and glutamine side chains, 
> the nitrogen is tetrahedral in the R-NH2 case or in the amino acid 
> N-terminus. A better example for two planar hydrogens would be =CH2 such as 
> in ethylene or vinyls.
> 
> 2)  The provided methods for adding hydrogens are not covering the whole 
> set of possibilities. In particular, it seems to me that three methods are 
> lacking, although admittedly they are less common:
> 
> a.   One tetrahedral hydrogen connected to atom i which is in turn 
> connected to two atoms j,k such that n is on the plane bisecting angle j-i-k; 
> n-i-j = n-i-k = 109.47 degrees; and dihedral n-i-j-l > 90 degrees. Example: 
> secondary amines R2NH. This case can be mimicked by method 2 with i,j,l atoms 
> so is perhaps superfluous.
> 
> b.  One planar hydrogen connected to atom i which is connected to only 
> one other atom j such that n-i-j = 120 degrees and n-i-j-k is trans. Example: 
> R2C=NH.
> 
> c.   One linear hydrogen such that n-i-j is a straight line. Example: #CH 
> where # is a triple bond.
> 
> 3)  I haven’t checked this, but can the k atom be a hydrogen added in an 
> earlier line of the same .hdb file?
> What do you say?
> Thanks,
> Ehud Schreiber.

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==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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[gmx-users] analysing helix dynamics

[jayant james]

Hi all,
During MD simulations of a protein,I find that there are two helices
switch periodically from being parallel and perpendicular to each
other.  I'd like to plot out the orientation of these two helices with
respect to each other, is there a command to extract this information?

JJ

http://www.chick.com/reading/tracts/1071/1071_01.asp
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[gmx-users] fatal occur occuring

[swati patel]

hello,
I am trying to simulate streptavidin tetramer-biotin complex.I ve
calculated Ligand topology from a sofware PRODRG using gromos87 force
fields.After solvating it,I am getting an error using grompp command

Fatal error:
Atomtype HW not found

can anyone provide me some help?

Thanx with anticipation.
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Re: [gmx-users] fatal occur occuring

[Justin A. Lemkul]

swati patel wrote:

hello,
I am trying to simulate streptavidin tetramer-biotin complex.I ve 
calculated Ligand topology from a sofware PRODRG using gromos87 force 
fields.After solvating it,I am getting an error using grompp command


Fatal error:
Atomtype HW not found

can anyone provide me some help?



The HW type is specific for the Gromos87 force field (i.e. gmx.ff in Gromacs), 
so if you're getting this fatal error, you're somehow mixing and matching force 
fields, likely between Gromos87 and Gromos96.


-Justin

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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] difference in force fields.

[swati patel]

helo justin,

yess since i am dealing with a complex,so i generated protein topology
using gromos96 43a1 force fields and for ligands,obtained topology using
PRODRG which uses gromos 87 force fields.

How to obtain similar force fields topologies since PRODRG only works with
gromos87 force fields and in gromacs i choosed optipn (9)i.e.gromos 96
force fields.??

thanx.
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Re: [gmx-users] difference in force fields.

[Justin A. Lemkul]

swati patel wrote:

helo justin,

yess since i am dealing with a complex,so i generated protein topology 
using gromos96 43a1 force fields and for ligands,obtained topology using 
PRODRG which uses gromos 87 force fields.


How to obtain similar force fields topologies since PRODRG only works 
with gromos87 force fields and in gromacs i choosed optipn (9)i.e.gromos 
96 force fields.??




This is not true.  There is a newer PRODRG server that creates topologies for 
Gromos96.  Their quality is not particularly high, as noted on this list on a 
weekly basis, and in the literature.  Please see the paper linked from:


http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips

-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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[gmx-users] problem in NVT equilibration

[Anushree Tripathi]

While running the command for NVT equilibration,I am getting one warning
for nvt.mdp i.e., The sum of the two largest charge group radii(2.334343)
is larger than rlist (1.00).But it is working and generating nvt.tpr
when I am using -maxwarn option.should I avoid this warning.Otherwise what
to do to get output without warning.Kindly guide me.
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Re: [gmx-users] problem in NVT equilibration

[Justin A. Lemkul]

Anushree Tripathi wrote:
While running the command for NVT equilibration,I am getting one warning 
for nvt.mdp i.e., The sum of the two largest charge group 
radii(2.334343) is larger than rlist (1.00).But it is working and 
generating nvt.tpr when I am using -maxwarn option.should I avoid this 
warning.Otherwise what to do to get output without warning.Kindly guide me.




http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb

The -maxwarn option should almost never be invoked.  The results of a forced 
grompp execution are often unpredictable or unstable.  The error messages exist 
for a reason.


-Justin

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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
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[gmx-users] PRODRG2.5 server not found.

[swati patel]

Helo Justin,

The link for prodrg 2.5 server is i.e.
http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta is 404 not found.How
should I proceed further?

Thanx.
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[gmx-users] problem obtaining similar force fields for protein and ligand

[swati patel]

Hello Users,

I am facing a problem in obtaining topologies for my ligand.I tried working
on acpype,bt it seems very complex to me.PRODRG is easy but it uses
gromos87 force field.PRODRG 2.5 is still not available for download.

can anyone suggest me how to obtain topologies for my protein and ligand
using same force fields?

thanks.
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[gmx-users] Regarding cosine content

[bipin singh]

Thanks for the reply...
I calculated principal components per protein using the command
g_anaeig -f md.xtc -s md.tpr -v eigenvec.trr -eig eigenval.xvg -comp
eigcomp.xvg -rmsf eigrmsf.xvg -2d 2dproj.xvg -proj proj.xvg -tu ns
-extr extr.pdb -filt filt.xtc -first 1 -last 2

Also please suggest how one can differentiate between the two
scenarios, when the high cosine content is due to random diffusion or
conformational changes ?


On Thu, Nov 17, 2011 at 17:34, Tsjerk Wassenaar  wrote:
> Hi Bipin,
>
> It seems one of the proteins is taking longer to reach an equilibrium.
> Maybe it is undergoing a conformational change?
> Did you calculate the principal components per protein, or for the
> joint trajectories? It would have been better to echo the commands you
> used on the list, because it might result in a different
> interpretation. I also made some comments on the list a short while
> ago regarding the interpretation of projections and cosine content.
> Maybe they can help you form a picture of what is happening :)
>
> Hope it helps,
>
> Tsjerk
>
>
> On Thu, Nov 17, 2011 at 12:22 PM, bipin singh  wrote:
>> Hello all,
>>
>> I have done PCA from 50ns long trajectory for two similar proteins
>> (length 180 aa and RMSD 0.2 A).
>> The equilibration time and final simulation condition were identical
>> for both the protein.
>> But when I checked the cosine content for PC1 for both proteins they
>> were 0.9 and 0.5 respectively.
>> What can be the reason for this huge difference in cosine content of
>> the two proteins ?
>>
>>
>> --
>> ---
>> Regards,
>> Bipin Singh
>> --
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
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--
---
Regards,
Bipin Singh



-- 
---
Regards,
Bipin Singh
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