[gmx-users] Separate removal of COM motion

[R]

Dear all
I am involved in a project where the target systems are lipid bilayers 
with and without different macromolecules embedded. In the past I did 
quite a lot of MD simulations of membrane systems always removing the 
COM motion of lipids and the solvent in separate groups. There are 
several discussions about this in the gmx users list (see for instance: 
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-September/108590.html) 
but I do not understand clearly the reason to do this. I am very 
interesting in determining diffusion coefficients, so the right removal 
of COM is key for my analysis. Can anyone explain why the global removal 
of COM for all the system might produce a lateral relative displacement 
of the bilayer with respect to the solvent in opposite directions (thus 
keeping the COM)? Is it guaranteed that this is solved by removing the 
COM separately for lipids and the solvent? When I have macromolecules 
embedded in the membrane, should I remove the COM of the macromolecules 
together with the lipids?


Thank you in advance for any help,

Ángel.

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[gmx-users] Long Simulations in Batch GMX 2018

[R]

Dear all,

I am doing a simulation of protein of my interest. I could run the simulation 
following the lysozyme tutorial. I am using 2018 version for gromacs.
To start with, I ran the simulation for 1 ns. I want to run long simulation 
though want to make sure that each trajectory files has a manageable size. 
Thus, I would like to run simulation in 5 ns batches i.e.

md_1.trr : 0-5ns
md_2.trr: 5-10ns
md_3.trr: 10-15ns like wise.

I am wondering how to run simulation like this in a loop of 5ns.
Any help would be highly appreciated.

Best,
Roli


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[gmx-users] Managing long simulations GMX 2018

[R]

 Dear all,


I plan to run a long simulation for my protein of interest. However, I want to 
write trajectory files in batches of 1ns simulation. Thus, my plan is to run 
simulation for 1ns (to get files like md_1.* e.g.) and then extend it further 
for another ns and output be written in md_2.* files. Having run 1ns 
simulation, I did following:


--> gmx convert-tpr -s md_1.tpr -extend 1000 -o md_2.tpr


--> gmx mdrun -s md_2.tpr -cpi md_1.cpt --noappend


However, this gave outputs:  state.cpt, state_prev.cpt, traj.part0002.trr, 
traj_comp.part0002.xtc, confout.part0002.gro, ener.part0002.edr.


My questions are following:


1) Am I following the right way to extend the simulation?


2) Is there a way to get output files with md_2.* names or I need to rename 
outputs to names I am interested in i.e. mv traj.part0002.trr md_2.trr etc?


3) Where can I read more about differences between state.cpt and state_prev.cpt?


I am back to simulations after years, last I used was gromacs 3.x series. 
Things are bit different now !

Thanks a lot for your help.
Best,
R
 






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[gmx-users] running parallel simulations on different of cores

[Muthukumaran R]

Dear gromacs users,
I have been working on gromacs package for performing md simulations.
recently i have started using cluster with 2 nodes with 64 cores each.
I am eager to know whether a job run on 32 cores for few ns and later i
continue the same job on 64 cores (or vice versa),  will show any
difference in the results in terms of energies or the  conformational
changes.

thanks in advance
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[gmx-users] add NaCl

[mohammad r]

Hi;
I've already converted topology and coordinate files which were generated with 
amber tools to .gro format. But now, when I want to add 100Mm NaCl to the 
system I get this error:
Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of file 
'c6m1_GMX.top'
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I think that it cannot recognize the solvent. How can I fix it?
Thank you, Mohammad
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[gmx-users] energy minimization

[mohammad r]

 Hi;
I've alreadyconverted the amber topology and coordinate files to gromacs 
format.But when I want to start running theenergy minimization first by using 
the grompp to generate .tpr file,I get this error:
Program gmx, VERSION5.0.2Source code 
file:/build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/toppush.c,line: 1353
Fatal error:Atomtype IP notfoundFor more informationand tips for 
troubleshooting, please check the GROMACSwebsite 
athttp://www.gromacs.org/Documentation/Errors
I think that itcannot recognize the atoms. I don't know how to fix it.
Best regards, Mohammad. 
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[gmx-users] energy minimization

[mohammad r]

Hi;
I've alreadyconverted the amber topology and coordinate files to gromacs 
format.But when I want to start running theenergy minimization first by using 
the grompp to generate .tpr file,I get this error:
Program gmx, VERSION5.0.2Source code 
file:/build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/toppush.c,line: 1353
Fatal error:Atomtype IP notfoundFor more informationand tips for 
troubleshooting, please check the GROMACSwebsite 
athttp://www.gromacs.org/Documentation/Errors
I think that itcannot recognize the atoms. I don't know how to fix it.
Best regards, Mohammad.
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[gmx-users] energy minimization

[mohammad r]

Hi;
I've alreadyconverted the amber topology and coordinate files to gromacs 
format.But when I want to start running theenergy minimization first by using 
the grompp to generate .tpr file,I get this error:
Program gmx, VERSION5.0.2Source code 
file:/build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/toppush.c,line: 1353
Fatal error:Atomtype IP notfoundFor more informationand tips for 
troubleshooting, please check the GROMACSwebsite 
athttp://www.gromacs.org/Documentation/Errors
I think that itcannot recognize the atoms. I don't know how to fix it.
Best regards, Mohammad.
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[gmx-users] energy minimization

[mohammad r]

 Hi;I've alreadyconverted the amber topology and coordinate files to gromacs 
format.But when I want to start running theenergy minimization first by using 
the grompp to generate .tpr file,I get this error:
Program gmx, VERSION5.0.2Source code 
file:/build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/toppush.c,line: 1353
Fatal error:Atomtype IP notfoundFor more informationand tips for 
troubleshooting, please check the GROMACSwebsite 
athttp://www.gromacs.org/Documentation/Errors
I think that itcannot recognize the atoms. I don't know how to fix it.
Best regards, Mohammad.

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[gmx-users] atom types IP and IM

[mohammad r]

Hi;
 I've used ff14sbamber force field to generate my system. As this force field 
doesn'texist in gromacs, I generated the first structure of my system withamber 
tools then I converted the topology and coordinate files intogromacs format by 
using acpype. (In the amber tools I've added NaClto my system). Now in the 
converted topology file I have these lines:
[ moleculetype ] ; molname nrexcl NA+ 1
[ atoms ] ; id_ at typeres nr residu name at name cg nr charge mass 1 IP 1 NA+ 
NA+ 1 1 22.9898
[ moleculetype ] ; molname nrexcl CL- 1
[ atoms ] ; id_ at typeres nr residu name at name cg nr charge mass 1 IM 1 CL- 
CL- 1 -1 35.45300
As we can see, wehave IP and IM atom types for Na+ and Cl- ions respectively. 
When Iwant to run energy minimization with the grompp command I get thiserror:
Fatal error: Atomtype IP not found For more information and tips for 
troubleshooting, please check the GROMACS  website at 
http://www.gromacs.org/Documentation/Errors
I think that itcannot recognize IP atom type. What should I do?
Thank you, Mohammad
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[gmx-users] acpype problem

[mohammad r]

 Hi;
 
  I want to convert amber topology and coordinate files into gromacs topology 
and coordinate file with the acpype command ( acpype -p FFF_AC.prmtop -x 
FFF_AC.inpcrd ), but when I type it, I get this error: acpype: command not 
found  
I've done the procedure mentioned in the website: 
https://code.google.com/p/acpype/wiki/HowToUse.   I've downloaded the acpype 
with svn checkout http://acpype.googlecode.com/svn/trunk/ acpype command. I 
installed it with sudo ln -s $PWD/acpype.py /usr/local/bin/acpype command. 
but when I try to use acpype -p FFF_AC.prmtop -x FFF_AC.inpcrd command, the 
error appeared .


  Thankyou, Mohammad.
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[gmx-users] force field

[mohammad r]

Hi;
I want to use ff14SB Amberprotein force field. But it isn't included in the 
gromacs force fields list.Is it possible to use this force field? How can I add 
it in?Thank you, Mohammad.
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Re: [gmx-users] force field

[mohammad r]

Thank you MaryamI want to use this force field in the first step of generating 
the topology file (pdb2gmx command in the force field shown after this 
command). Is it possible? and unfortunately I don't know how to find the 
necessary files of this force field. I searched a lot but I didn't succeed.  
I have another question, is it possible to acetylate or ammoniate a peptide 
with gromacs?
thank you, M. 


 On Sunday, August 9, 2015 8:17 PM, Maryam Kowsar maryam.kow...@gmail.com 
wrote:
   

 let me modify my previous message: in the g_x2top command, not grompp :-)
On Sun, Aug 9, 2015 at 8:14 PM, Maryam Kowsar maryam.kow...@gmail.com wrote:

Hi Mohammad,
Yes that's possible. You should just have the necessary files of your desired 
forcefield(.atp,.itp,...), and put them in a folder. in the grompp command just 
add -ff folder name. that's all! It will use your forcefield instead of the 
present forcefields in gromacs.
Regards,-Maryam
On Sun, Aug 9, 2015 at 5:57 PM, mohammad r mohammad.r0...@yahoo.com wrote:

Hi;
I want to use ff14SB Amberprotein force field. But it isn't included in the 
gromacs force fields list.Is it possible to use this force field? How can I add 
it in?Thank you, Mohammad.
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[gmx-users] adding lipids

[mohammad r]

Hi everybody;
I have a cubic box with a peptide in its center (the .gro file). Now I want to 
add some lipids (e.g. 3 molecules)(I have the .gro and .top and .pdb files of 
the lipid) to this box. But I don't know how to do it.I think that "gmx 
insert-molecules" command will help, but again I don't know how to use it, 
which parameters are needed.
Thank you, Mohammad.
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[gmx-users] adding lipids

[mohammad r]

Hi everybody;
I have a cubic box with a peptide in its center (the .gro file). Now I want to 
add some lipids (e.g. 3 molecules)(I have the .gro and .top and .pdb files of 
the lipid) to this box. But I don't know how to do it.I think that "gmx 
insert-molecules" command will help, but again I don't know how to use it, 
which parameters are needed.
Thank you, Mohammad.
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[gmx-users] installing GROMACS

[mohammad r]

Hi;

I tried to install GROMACS using "Installation guide for GROMACS 5.0.5" in the 
gromacs.org, but I got an error after typing "cmake .. " line, then I tried 
"sudo apt-get install gromacs" command, it installed the gromacs-4.6.5 but I 
want the gromacs-5.0.5.
what should I do?

Thank you, Mohammad.
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[gmx-users] installing gromacs-5.0.5

[mohammad r]

Hello everybody;
I want to install gromacs-5.0.5 in ubuntu-14.04 using the installation 
instruction in the website "gromacs.org", but in the "cmake .. 
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON" line I got this error:
-- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration
CMake Error at cmake/gmxTestSimd.cmake:160 (message):
  Cannot find compiler flags for 128 bit AVX with FMA support.  Use a newer
  compiler, or choose SSE4.1 SIMD (slower).
Call Stack (most recent call first):
  CMakeLists.txt:720 (gmx_test_simd)


-- Configuring incomplete, errors occurred!

I've updated the gcc compiler but again this error occurred. 
I used the "sudo apt-get install gromacs" command but this installed the 
gromacs-4.6.5 and I want gromacs-5.0.5.can you help me, please?
Thank you, Mohammad.

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[gmx-users] Equilibration fails only when run from script

[R Corey]

Hello

I am running a series of FEP MD simulations using Gromacs 5.0.4, for each a
steepest descents minimization, NVT equil, NPT equil and production run,
all controlled by a central script. However, only about 50% of the runs get
through the NVT equilibration without crashing - crash error as below:

Fatal error:
3 particles communicated to PME rank 0 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.

However, the weird thing is that if I re-run the script the next day,
choosing only failed jobs to rerun, some of them now work fine. And if I
simply mdrun each tpr from the command line it runs fine too.

Is this expected, that a tpr file for an NVT equilibration will crash one
day but run fine the next?

Cheers

Robin

-- 
*Robin Corey*
PhD Student
School of Biochemistry
University of Bristol
University Walk
Bristol BS8 1TD
UK
r.co...@bristol.ac.uk
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[gmx-users] convert amber files to gromacs

[mohammad r]

Hi everybody,


 
I want to convert the topology and coordinate files fromamber to gromacs 
format. I used acpype bu it didn’t work properly (actually mysystem is 
consisted of some lipids in a water-protein system but when I convertthe files 
via acpype, the backbone is consisted of a mass solvated in water,indeed in the 
converted topology file in the molecule types section the proteinand lipids 
assumed to be one mass and two molecule types exist: the water andthat mass), 
also I downloaded the “ambconv.tgz” from gromacs website but I don’tknow how to 
work with that. Can you please help me how to conver my files?


 
Thank you, Mohammad.

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Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

[Husen R]

On Thu, Jun 16, 2016 at 2:32 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> On Thu, Jun 16, 2016 at 9:30 AM Husen R <hus...@gmail.com> wrote:
>
> > Hi,
> >
> > Thank you for your reply !
> >
> > md_test.xtc is exist and writable.
> >
>
> OK, but it needs to be seen that way from the set of compute nodes you are
> using, and organizing that is up to you and your job scheduler, etc.
>
>
> > I tried to restart from checkpoint file by excluding other node than
> > compute-node and it works.
> >
>
> Go do that, then :-)
>

I'm building a simple system that can respond to node failure. if failure
occured on node A, than the application has to be restarted and that node
has to be excluded.
this should apply to all node including this 'compute-node'.

>
>
> > only '--exclude=compute-node' that produces this error.
> >
>
> Then there's something about that node that is special with respect to the
> file system - there's nothing about any particular node that GROMACS cares
> about.
>

> Mark
>
>
> > is this has the same issue with this thread ?
> > http://comments.gmane.org/gmane.science.biology.gromacs.user/40984
> >
> > regards,
> >
> > Husen
> >
> > On Thu, Jun 16, 2016 at 2:20 PM, Mark Abraham <mark.j.abra...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > The stuff about different nodes or numbers of nodes doesn't matter -
> it's
> > > merely an advisory note from mdrun. mdrun failed when it tried to
> operate
> > > upon md_test.xtc, so perhaps you need to consider whether the file
> > exists,
> > > is writable, etc.
> > >
> > > Mark
> > >
> > > On Thu, Jun 16, 2016 at 6:48 AM Husen R <hus...@gmail.com> wrote:
> > >
> > > > Hi all,
> > > >
> > > > I got the following error message when I tried to restart gromacs
> > > > simulation from checkpoint file.
> > > > I restart the simulation using fewer nodes and processes, and also I
> > > > exclude one node using '--exclude=' option (in slurm) for
> experimental
> > > > purpose.
> > > >
> > > > I'm sure fewer nodes and processes are not the cause of this error
> as I
> > > > already test that.
> > > > I have checked that the cause of this error is '--exclude=' usage. I
> > > > excluded 1 node named 'compute-node' when restart from checkpoint (at
> > > first
> > > > run, I use all node including 'compute-node').
> > > >
> > > >
> > > > it seems that at first run, the submit job script was built at
> > > > compute-node. So, at restart, build user mismatch appeared because
> > > > compute-node was not found (excluded).
> > > >
> > > > Am I right ? is this behavior normal ?
> > > > or is that a way to avoid this, so I can freely restart from
> checkpoint
> > > > using any nodes without limitation.
> > > >
> > > > thank you in advance
> > > >
> > > > Regards,
> > > >
> > > >
> > > > Husen
> > > >
> > > > ==restart script=
> > > > #!/bin/bash
> > > > #SBATCH -J ayo
> > > > #SBATCH -o md%j.out
> > > > #SBATCH -A necis
> > > > #SBATCH -N 2
> > > > #SBATCH -n 16
> > > > #SBATCH --exclude=compute-node
> > > > #SBATCH --time=144:00:00
> > > > #SBATCH --mail-user=hus...@gmail.com
> > > > #SBATCH --mail-type=begin
> > > > #SBATCH --mail-type=end
> > > >
> > > > mpirun gmx_mpi mdrun -cpi md_test.cpt -deffnm md_test
> > > > =
> > > >
> > > >
> > > >
> > > >
> > > > ==output
> error
> > > > Reading checkpoint file md_test.cpt generated: Wed Jun 15 16:30:44
> 2016
> > > >
> > > >
> > > >   Build time mismatch,
> > > > current program: Sel Apr  5 13:37:32 WIB 2016
> > > > checkpoint file: Rab Apr  6 09:44:51 WIB 2016
> > > >
> > > >   Build user mismatch,
> > > > current program: pro@head-node [CMAKE]
> > > > checkpoint file: pro@compute-node [CMAKE]
> > > >
> > > >   #ranks mismatch,
> > > > current program: 16
> 

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

[Husen R]

On Thu, Jun 16, 2016 at 4:01 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> There's just nothing special about any node at run time.
>
> Your script looks like it is building GROMACS fresh each time - there's no
> need to do that,


which part of my script ?
I always use this command to restart from checkpoint file -->  "mpirun
gmx_mpi mdrun -cpi [name].cpt -deffnm [name]".
as far as I know -cpi option is used to refer to checkpoint file as input
file.
 what I have to change in my script ?


but the fact that the node name is showing up in the check
> that takes place when the checkpoint is read is not relevant to the
> problem.
>
> Mark
>
> On Thu, Jun 16, 2016 at 9:46 AM Husen R <hus...@gmail.com> wrote:
>
> > On Thu, Jun 16, 2016 at 2:32 PM, Mark Abraham <mark.j.abra...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > On Thu, Jun 16, 2016 at 9:30 AM Husen R <hus...@gmail.com> wrote:
> > >
> > > > Hi,
> > > >
> > > > Thank you for your reply !
> > > >
> > > > md_test.xtc is exist and writable.
> > > >
> > >
> > > OK, but it needs to be seen that way from the set of compute nodes you
> > are
> > > using, and organizing that is up to you and your job scheduler, etc.
> > >
> > >
> > > > I tried to restart from checkpoint file by excluding other node than
> > > > compute-node and it works.
> > > >
> > >
> > > Go do that, then :-)
> > >
> >
> > I'm building a simple system that can respond to node failure. if failure
> > occured on node A, than the application has to be restarted and that node
> > has to be excluded.
> > this should apply to all node including this 'compute-node'.
> >
> > >
> > >
> > > > only '--exclude=compute-node' that produces this error.
> > > >
> > >
> > > Then there's something about that node that is special with respect to
> > the
> > > file system - there's nothing about any particular node that GROMACS
> > cares
> > > about.
> > >
> >
> > > Mark
> > >
> > >
> > > > is this has the same issue with this thread ?
> > > > http://comments.gmane.org/gmane.science.biology.gromacs.user/40984
> > > >
> > > > regards,
> > > >
> > > > Husen
> > > >
> > > > On Thu, Jun 16, 2016 at 2:20 PM, Mark Abraham <
> > mark.j.abra...@gmail.com>
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > The stuff about different nodes or numbers of nodes doesn't matter
> -
> > > it's
> > > > > merely an advisory note from mdrun. mdrun failed when it tried to
> > > operate
> > > > > upon md_test.xtc, so perhaps you need to consider whether the file
> > > > exists,
> > > > > is writable, etc.
> > > > >
> > > > > Mark
> > > > >
> > > > > On Thu, Jun 16, 2016 at 6:48 AM Husen R <hus...@gmail.com> wrote:
> > > > >
> > > > > > Hi all,
> > > > > >
> > > > > > I got the following error message when I tried to restart gromacs
> > > > > > simulation from checkpoint file.
> > > > > > I restart the simulation using fewer nodes and processes, and
> also
> > I
> > > > > > exclude one node using '--exclude=' option (in slurm) for
> > > experimental
> > > > > > purpose.
> > > > > >
> > > > > > I'm sure fewer nodes and processes are not the cause of this
> error
> > > as I
> > > > > > already test that.
> > > > > > I have checked that the cause of this error is '--exclude='
> usage.
> > I
> > > > > > excluded 1 node named 'compute-node' when restart from checkpoint
> > (at
> > > > > first
> > > > > > run, I use all node including 'compute-node').
> > > > > >
> > > > > >
> > > > > > it seems that at first run, the submit job script was built at
> > > > > > compute-node. So, at restart, build user mismatch appeared
> because
> > > > > > compute-node was not found (excluded).
> > > > > >
> > > > > > Am I right ? is this behavior normal ?
> > > > > > or is that a way to avoid

Re: [gmx-users] How does gromacs checkpoint works

[Husen R]

Hi,

Could you tell me the location of the code ?
is this the location of the code ->
gromacs-5.1.2/src/gromacs/gmxlib/checkpoint.cpp ?

regards,

Husen

On Thu, Jun 23, 2016 at 2:23 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> There's only the code. All you have to do is write down everything that you
> were going to need to read to do the next step (unless it's from the .tpr).
> Add some checksums of the last pieces of output files, so you can help the
> user not mangle their files upon restart. Decide how you're going to
> coordinate all your ranks/cores choosing to checkpoint at the same time.
> Pick a portable file format.
>
> Mark
>
> On Thu, Jun 23, 2016 at 4:15 AM Husen R <hus...@gmail.com> wrote:
>
> > Hi all,
> >
> > For academic purpose, I'm wondering how does checkpoint feature in
> Gromacs
> > works ?
> > is there any resource/tutorial that I can learn ?
> >
> >
> > Thank you in advance,
> >
> >
> > Husen
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

[Husen R]

Hi,

I still unable to find out the cause of the fatal error.
Previously, gromacs is installed in every nodes. That's the cause Build
time mismatch and Build user mismatch appeared.
Now, Build time mismatch and Build user mismatch issues are solved by
installing Gromacs in shared directory.

I have tried to install gromacs in one node only (not in shared directory),
but the error appeared.


this is the error message if I exclude compute-node
"--exclude=compute-node" from nodelist in slurm sbatch. excluding other
nodes works fine.


=
GROMACS:  gmx mdrun, VERSION 5.1.2
Executable:   /mirror/source/gromacs/bin/gmx_mpi
Data prefix:  /mirror/source/gromacs
Command line:
  gmx_mpi mdrun -cpi md_gmx.cpt -deffnm md_gmx


Running on 2 nodes with total 8 cores, 16 logical cores
  Cores per node:4
  Logical cores per node:8
Hardware detected on host head-node (the node of MPI rank 0):
  CPU info:
Vendor: GenuineIntel
Brand:  Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz
SIMD instructions most likely to fit this hardware: AVX_256
SIMD instructions selected at GROMACS compile time: AVX_256

Reading file md_gmx.tpr, VERSION 5.1.2 (single precision)
Changing nstlist from 10 to 20, rlist from 1 to 1.03


Reading checkpoint file md_gmx.cpt generated: Thu Jun 23 12:54:02 2016


  #ranks mismatch,
current program: 16
checkpoint file: 24

  #PME-ranks mismatch,
current program: -1
checkpoint file: 6

GROMACS patchlevel, binary or parallel settings differ from previous run.
Continuation is exact, but not guaranteed to be binary identical.


---
Program gmx mdrun, VERSION 5.1.2
Source code file:
/home/necis/gromacsinstall/gromacs-5.1.2/src/gromacs/gmxlib/checkpoint.cpp,
line: 2216

Fatal error:
Truncation of file md_gmx.xtc failed. Cannot do appending because of this
failure.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


On Thu, Jun 16, 2016 at 6:23 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> On Thu, Jun 16, 2016 at 12:24 PM Husen R <hus...@gmail.com> wrote:
>
> > On Thu, Jun 16, 2016 at 4:01 PM, Mark Abraham <mark.j.abra...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > There's just nothing special about any node at run time.
> > >
> > > Your script looks like it is building GROMACS fresh each time - there's
> > no
> > > need to do that,
> >
> >
> > which part of my script ?
> >
>
> I can't tell how your script is finding its GROMACS installations, but the
> advisory message says precisely that your runs are finding different
> installations...
>
>   Build time mismatch,
> current program: Sel Apr  5 13:37:32 WIB 2016
> checkpoint file: Rab Apr  6 09:44:51 WIB 2016
>
>   Build user mismatch,
> current program: pro@head-node [CMAKE]
> checkpoint file: pro@compute-node [CMAKE]
>
> This reinforces my impression that the view of your file system available
> at the start of the job script is varying with your choice of node subsets.
>
>
> > I always use this command to restart from checkpoint file -->  "mpirun
> > gmx_mpi mdrun -cpi [name].cpt -deffnm [name]".
> > as far as I know -cpi option is used to refer to checkpoint file as input
> > file.
> >  what I have to change in my script ?
> >
>
> Nothing about that aspect. But clearly your first run and the restart
> simulating loss of a node are finding different gmx_mpi binaries from their
> respective environments. This is not itself a problem, but it's probably
> not what you intend, and may be symptomatic of the same issue that leads to
> md_test.xtc not being accessible.
>
> Mark
>
>
> >
> > but the fact that the node name is showing up in the check
> > > that takes place when the checkpoint is read is not relevant to the
> > > problem.
> > >
> > > Mark
> > >
> > > On Thu, Jun 16, 2016 at 9:46 AM Husen R <hus...@gmail.com> wrote:
> > >
> > > > On Thu, Jun 16, 2016 at 2:32 PM, Mark Abraham <
> > mark.j.abra...@gmail.com>
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > On Thu, Jun 16, 2016 at 9:30 AM Husen R <hus...@gmail.com> wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > Thank you for your reply !
> > > > > >
> >

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

[Husen R]

Hi,

I'm wondering, if I use gromacs in cluster environment, do I have to
install gromacs in every nodes (at /usr/local/gromacs in every nodes) ?
or is it enough to install gromacs in one node (example,in head-node) only
?

Regards,

Husen



On Thu, Jun 23, 2016 at 3:41 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> The only explanation is that that file is not in fact properly accessible
> if rank 0 is placed other than on "compute-node," which means your
> organization of file system / slurm / etc. aren't good enough for what
> you're doing.
>
> Mark
>
> On Thu, Jun 23, 2016 at 10:15 AM Husen R <hus...@gmail.com> wrote:
>
> > Hi,
> >
> > I still unable to find out the cause of the fatal error.
> > Previously, gromacs is installed in every nodes. That's the cause Build
> > time mismatch and Build user mismatch appeared.
> > Now, Build time mismatch and Build user mismatch issues are solved by
> > installing Gromacs in shared directory.
> >
> > I have tried to install gromacs in one node only (not in shared
> directory),
> > but the error appeared.
> >
> >
> > this is the error message if I exclude compute-node
> > "--exclude=compute-node" from nodelist in slurm sbatch. excluding other
> > nodes works fine.
> >
> >
> >
> >
> =
> > GROMACS:  gmx mdrun, VERSION 5.1.2
> > Executable:   /mirror/source/gromacs/bin/gmx_mpi
> > Data prefix:  /mirror/source/gromacs
> > Command line:
> >   gmx_mpi mdrun -cpi md_gmx.cpt -deffnm md_gmx
> >
> >
> > Running on 2 nodes with total 8 cores, 16 logical cores
> >   Cores per node:4
> >   Logical cores per node:8
> > Hardware detected on host head-node (the node of MPI rank 0):
> >   CPU info:
> > Vendor: GenuineIntel
> > Brand:  Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz
> > SIMD instructions most likely to fit this hardware: AVX_256
> > SIMD instructions selected at GROMACS compile time: AVX_256
> >
> > Reading file md_gmx.tpr, VERSION 5.1.2 (single precision)
> > Changing nstlist from 10 to 20, rlist from 1 to 1.03
> >
> >
> > Reading checkpoint file md_gmx.cpt generated: Thu Jun 23 12:54:02 2016
> >
> >
> >   #ranks mismatch,
> > current program: 16
> > checkpoint file: 24
> >
> >   #PME-ranks mismatch,
> > current program: -1
> > checkpoint file: 6
> >
> > GROMACS patchlevel, binary or parallel settings differ from previous run.
> > Continuation is exact, but not guaranteed to be binary identical.
> >
> >
> > ---
> > Program gmx mdrun, VERSION 5.1.2
> > Source code file:
> >
> /home/necis/gromacsinstall/gromacs-5.1.2/src/gromacs/gmxlib/checkpoint.cpp,
> > line: 2216
> >
> > Fatal error:
> > Truncation of file md_gmx.xtc failed. Cannot do appending because of this
> > failure.
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> >
> 
> >
> > On Thu, Jun 16, 2016 at 6:23 PM, Mark Abraham <mark.j.abra...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > On Thu, Jun 16, 2016 at 12:24 PM Husen R <hus...@gmail.com> wrote:
> > >
> > > > On Thu, Jun 16, 2016 at 4:01 PM, Mark Abraham <
> > mark.j.abra...@gmail.com>
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > There's just nothing special about any node at run time.
> > > > >
> > > > > Your script looks like it is building GROMACS fresh each time -
> > there's
> > > > no
> > > > > need to do that,
> > > >
> > > >
> > > > which part of my script ?
> > > >
> > >
> > > I can't tell how your script is finding its GROMACS installations, but
> > the
> > > advisory message says precisely that your runs are finding different
> > > installations...
> > >
> > >   Build time mismatch,
> > > current program: Sel Apr  5 13:37:32 WIB 2016
> > > checkpoint file: Rab Apr  6 09:44:51 WIB 2016
> > >
> > >   Build user mismatch,
> > > current program: pro@head-

Re: [gmx-users] How does gromacs checkpoint works

[Husen R]

Hi Mark,


Thank you very much!

Regards,


Husen

On Thu, Jun 23, 2016 at 3:42 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Yes
>
> On Thu, Jun 23, 2016 at 9:54 AM Husen R <hus...@gmail.com> wrote:
>
> > Hi,
> >
> > Could you tell me the location of the code ?
> > is this the location of the code ->
> > gromacs-5.1.2/src/gromacs/gmxlib/checkpoint.cpp ?
> >
> > regards,
> >
> > Husen
> >
> > On Thu, Jun 23, 2016 at 2:23 PM, Mark Abraham <mark.j.abra...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > There's only the code. All you have to do is write down everything that
> > you
> > > were going to need to read to do the next step (unless it's from the
> > .tpr).
> > > Add some checksums of the last pieces of output files, so you can help
> > the
> > > user not mangle their files upon restart. Decide how you're going to
> > > coordinate all your ranks/cores choosing to checkpoint at the same
> time.
> > > Pick a portable file format.
> > >
> > > Mark
> > >
> > > On Thu, Jun 23, 2016 at 4:15 AM Husen R <hus...@gmail.com> wrote:
> > >
> > > > Hi all,
> > > >
> > > > For academic purpose, I'm wondering how does checkpoint feature in
> > > Gromacs
> > > > works ?
> > > > is there any resource/tutorial that I can learn ?
> > > >
> > > >
> > > > Thank you in advance,
> > > >
> > > >
> > > > Husen
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
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> > >
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> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
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> >
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> > posting!
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> >
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[gmx-users] How does gromacs checkpoint works

[Husen R]

Hi all,

For academic purpose, I'm wondering how does checkpoint feature in Gromacs
works ?
is there any resource/tutorial that I can learn ?


Thank you in advance,


Husen
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[gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

[Husen R]

Hi all,

I got the following error message when I tried to restart gromacs
simulation from checkpoint file.
I restart the simulation using fewer nodes and processes, and also I
exclude one node using '--exclude=' option (in slurm) for experimental
purpose.

I'm sure fewer nodes and processes are not the cause of this error as I
already test that.
I have checked that the cause of this error is '--exclude=' usage. I
excluded 1 node named 'compute-node' when restart from checkpoint (at first
run, I use all node including 'compute-node').


it seems that at first run, the submit job script was built at
compute-node. So, at restart, build user mismatch appeared because
compute-node was not found (excluded).

Am I right ? is this behavior normal ?
or is that a way to avoid this, so I can freely restart from checkpoint
using any nodes without limitation.

thank you in advance

Regards,


Husen

==restart script=
#!/bin/bash
#SBATCH -J ayo
#SBATCH -o md%j.out
#SBATCH -A necis
#SBATCH -N 2
#SBATCH -n 16
#SBATCH --exclude=compute-node
#SBATCH --time=144:00:00
#SBATCH --mail-user=hus...@gmail.com
#SBATCH --mail-type=begin
#SBATCH --mail-type=end

mpirun gmx_mpi mdrun -cpi md_test.cpt -deffnm md_test
=




==output error
Reading checkpoint file md_test.cpt generated: Wed Jun 15 16:30:44 2016


  Build time mismatch,
current program: Sel Apr  5 13:37:32 WIB 2016
checkpoint file: Rab Apr  6 09:44:51 WIB 2016

  Build user mismatch,
current program: pro@head-node [CMAKE]
checkpoint file: pro@compute-node [CMAKE]

  #ranks mismatch,
current program: 16
checkpoint file: 24

  #PME-ranks mismatch,
current program: -1
checkpoint file: 6

GROMACS patchlevel, binary or parallel settings differ from previous run.
Continuation is exact, but not guaranteed to be binary identical.


---
Program gmx mdrun, VERSION 5.1.2
Source code file:
/home/pro/gromacs-5.1.2/src/gromacs/gmxlib/checkpoint.cpp, line: 2216

Fatal error:
Truncation of file md_test.xtc failed. Cannot do appending because of this
failure.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

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Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

[Husen R]

this is the rest of the error message..
regards,

Husen




Halting parallel program gmx mdrun on rank 0 out of 16
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Fatal error in PMPI_Bcast: Unknown error class, error stack:
PMPI_Bcast(1635)..: MPI_Bcast(buf=0xcd9ed8, count=4,
MPI_BYTE, root=0, MPI_COMM_WORLD) failed
MPIR_Bcast_impl(1477).:
MPIR_Bcast(1501)..:
MPIR_Bcast_intra(1272):
MPIR_SMP_Bcast(1104)..:
MPIR_Bcast_binomial(256)..:
MPIDU_Complete_posted_with_error(1189): Process failed
MPIR_SMP_Bcast()..:
MPIR_Bcast_binomial(327)..: Failure during collective
Fatal error in PMPI_Bcast: Other MPI error, error stack:
PMPI_Bcast(1635): MPI_Bcast(buf=0x1858e78, count=4, MPI_BYTE,
root=0, MPI_COMM_WORLD) failed
MPIR_Bcast_impl(1477)...:
MPIR_Bcast(1501):
MPIR_Bcast_intra(1272)..:
MPIR_SMP_Bcast():
MPIR_Bcast_binomial(327): Failure during collective
Fatal error in PMPI_Bcast: Other MPI error, error stack:
PMPI_Bcast(1635): MPI_Bcast(buf=0x24f7e78, count=4, MPI_BYTE,
root=0, MPI_COMM_WORLD) failed
MPIR_Bcast_impl(1477)...:
MPIR_Bcast(1501):
MPIR_Bcast_intra(1272)..:
MPIR_SMP_Bcast():
MPIR_Bcast_binomial(327): Failure during collective
Fatal error in PMPI_Bcast: Other MPI error, error stack:
PMPI_Bcast(1635): MPI_Bcast(buf=0xb21e78, count=4, MPI_BYTE,
root=0, MPI_COMM_WORLD) failed
MPIR_Bcast_impl(1477)...:
MPIR_Bcast(1501):
MPIR_Bcast_intra(1272)..:
MPIR_SMP_Bcast():
MPIR_Bcast_binomial(327): Failure during collective
Fatal error in PMPI_Bcast: Other MPI error, error stack:
PMPI_Bcast(1635): MPI_Bcast(buf=0x15fbe78, count=4, MPI_BYTE,
root=0, MPI_COMM_WORLD) failed
MPIR_Bcast_impl(1477)...:
MPIR_Bcast(1501):
MPIR_Bcast_intra(1272)..:
MPIR_SMP_Bcast():
MPIR_Bcast_binomial(327): Failure during collective

===
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 6983 RUNNING AT head-node
=   EXIT CODE: 1
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===

On Thu, Jun 16, 2016 at 11:48 AM, Husen R <hus...@gmail.com> wrote:

> Hi all,
>
> I got the following error message when I tried to restart gromacs
> simulation from checkpoint file.
> I restart the simulation using fewer nodes and processes, and also I
> exclude one node using '--exclude=' option (in slurm) for experimental
> purpose.
>
> I'm sure fewer nodes and processes are not the cause of this error as I
> already test that.
> I have checked that the cause of this error is '--exclude=' usage. I
> excluded 1 node named 'compute-node' when restart from checkpoint (at first
> run, I use all node including 'compute-node').
>
>
> it seems that at first run, the submit job script was built at
> compute-node. So, at restart, build user mismatch appeared because
> compute-node was not found (excluded).
>
> Am I right ? is this behavior normal ?
> or is that a way to avoid this, so I can freely restart from checkpoint
> using any nodes without limitation.
>
> thank you in advance
>
> Regards,
>
>
> Husen
>
> ==restart script=
> #!/bin/bash
> #SBATCH -J ayo
> #SBATCH -o md%j.out
> #SBATCH -A necis
> #SBATCH -N 2
> #SBATCH -n 16
> #SBATCH --exclude=compute-node
> #SBATCH --time=144:00:00
> #SBATCH --mail-user=hus...@gmail.com
> #SBATCH --mail-type=begin
> #SBATCH --mail-type=end
>
> mpirun gmx_mpi mdrun -cpi md_test.cpt -deffnm md_test
> =
>
>
>
>
> ==output error
> Reading checkpoint file md_test.cpt generated: Wed Jun 15 16:30:44 2016
>
>
>   Build time mismatch,
> current program: Sel Apr  5 13:37:32 WIB 2016
> checkpoint file: Rab Apr  6 09:44:51 WIB 2016
>
>   Build user mismatch,
> current program: pro@head-node [CMAKE]
> checkpoint file: pro@compute-node [CMAKE]
>
>   #ranks mismatch,
> current program: 16
> checkpoint file: 24
>
>   #PME-ranks mismatch,
> current program: -1
> checkpoint file: 6
>
> GROMACS patchlevel, binary or parallel settings differ from previous run.
> Continuation is exact, but not guaranteed to be binary identical.
>
>
> ---
> Program gmx mdrun, VERSION 5.1.2
> Source code file:
> /home/pro/gromacs-5.1.2/src/gromacs/gmxlib/checkpoint.cpp, line: 2216
&g

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

[Husen R]

Hi,

Thank you for your reply !

md_test.xtc is exist and writable.
I tried to restart from checkpoint file by excluding other node than
compute-node and it works.
only '--exclude=compute-node' that produces this error.

is this has the same issue with this thread ?
http://comments.gmane.org/gmane.science.biology.gromacs.user/40984

regards,

Husen

On Thu, Jun 16, 2016 at 2:20 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> The stuff about different nodes or numbers of nodes doesn't matter - it's
> merely an advisory note from mdrun. mdrun failed when it tried to operate
> upon md_test.xtc, so perhaps you need to consider whether the file exists,
> is writable, etc.
>
> Mark
>
> On Thu, Jun 16, 2016 at 6:48 AM Husen R <hus...@gmail.com> wrote:
>
> > Hi all,
> >
> > I got the following error message when I tried to restart gromacs
> > simulation from checkpoint file.
> > I restart the simulation using fewer nodes and processes, and also I
> > exclude one node using '--exclude=' option (in slurm) for experimental
> > purpose.
> >
> > I'm sure fewer nodes and processes are not the cause of this error as I
> > already test that.
> > I have checked that the cause of this error is '--exclude=' usage. I
> > excluded 1 node named 'compute-node' when restart from checkpoint (at
> first
> > run, I use all node including 'compute-node').
> >
> >
> > it seems that at first run, the submit job script was built at
> > compute-node. So, at restart, build user mismatch appeared because
> > compute-node was not found (excluded).
> >
> > Am I right ? is this behavior normal ?
> > or is that a way to avoid this, so I can freely restart from checkpoint
> > using any nodes without limitation.
> >
> > thank you in advance
> >
> > Regards,
> >
> >
> > Husen
> >
> > ==restart script=
> > #!/bin/bash
> > #SBATCH -J ayo
> > #SBATCH -o md%j.out
> > #SBATCH -A necis
> > #SBATCH -N 2
> > #SBATCH -n 16
> > #SBATCH --exclude=compute-node
> > #SBATCH --time=144:00:00
> > #SBATCH --mail-user=hus...@gmail.com
> > #SBATCH --mail-type=begin
> > #SBATCH --mail-type=end
> >
> > mpirun gmx_mpi mdrun -cpi md_test.cpt -deffnm md_test
> > =
> >
> >
> >
> >
> > ==output error
> > Reading checkpoint file md_test.cpt generated: Wed Jun 15 16:30:44 2016
> >
> >
> >   Build time mismatch,
> > current program: Sel Apr  5 13:37:32 WIB 2016
> > checkpoint file: Rab Apr  6 09:44:51 WIB 2016
> >
> >   Build user mismatch,
> > current program: pro@head-node [CMAKE]
> > checkpoint file: pro@compute-node [CMAKE]
> >
> >   #ranks mismatch,
> > current program: 16
> > checkpoint file: 24
> >
> >   #PME-ranks mismatch,
> > current program: -1
> > checkpoint file: 6
> >
> > GROMACS patchlevel, binary or parallel settings differ from previous run.
> > Continuation is exact, but not guaranteed to be binary identical.
> >
> >
> > ---
> > Program gmx mdrun, VERSION 5.1.2
> > Source code file:
> > /home/pro/gromacs-5.1.2/src/gromacs/gmxlib/checkpoint.cpp, line: 2216
> >
> > Fatal error:
> > Truncation of file md_test.xtc failed. Cannot do appending because of
> this
> > failure.
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > ---
> > 
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
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[gmx-users] DMF molecule

[mohammad r]

Hi everybody,
I have the DMF pdb file and I want to import it to gromacs by pdb2gmx command, 
but the residues are not included in none of the forcefields. can you please 
help me figure this out?
Thank you, Mohammad.
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[gmx-users] DSSP secondary structure

[mohammad r]

Hi,
I used the "gmx do_dssp" command to get the secondary structure of the protein 
during the simulation but the resolution of the resulted .xpm file is very low. 
how can I increase its resolution?
Thank you, Mohammad.
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[gmx-users] modeling CNT, center of mass velocity, energy minimization

[mohammad r]

Hi GROMACS users,


  I have some questions:  1-  Can I model a carbonnanotube (CNT) 
conveying fluid in GROMACS subjected to a magnetic field?2-  How can I 
check the centerof mass velocity of my system?3-  I want to calculate 
volumeand water self diffusion coefficient for 1ns, can the energy 
minimizationprocess do it? Or the equilibrium processes can do it? I want to 
draw theparameters versus time.  Thank you, Mohammad.

  
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Re: [gmx-users] DSSP secondary structure

[mohammad r]

I changed and reduced the ratio but the xpm file was not changed at all.
 

On Sunday, February 14, 2016 5:05 PM, Justin Lemkul <jalem...@vt.edu> wrote:
 

 

On 2/14/16 1:54 AM, mohammad r wrote:
> Thank you Justin,
>
> I used xpm2ps command with below m2p file but the resolution was not changed.
> I've attached the xpm file, even the legend can't be seen.
> is there anyway to get the result file in pdf format?
>
> m2p file (I found it in the gromacs website):
>

> xbox = 2.0 ; x‐size of a matrix element
> ybox = 2.0 ; y‐size of a matrix element

You have a rectangular matrix, with the x-dimension being much longer than the 
y-dimension.  If you set these two values to be the same, what happens to the 
size of the rectangle?  It gets uniformly scaled.  So naturally that 
accomplishes nothing.  What you need to do is reduce the ratio of xbox/ybox.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] DSSP secondary structure

[mohammad r]

Thank you Justin,
 I did it by using xpm2ps and ps2pdf commands. Now I want to ask, is there any 
way to calculate the percentage of a-helical structure of a protein during 
simulation? Indeed DSSP visualize it but I want to calculate it exactly.
Thanks, Mohammad.
 

On Monday, February 15, 2016 6:31 PM, Justin Lemkul <jalem...@vt.edu> wrote:
 

 

On 2/15/16 1:31 AM, mohammad r wrote:
> I changed and reduced the ratio but the xpm file was not changed at all.
>

Unfortunately there's not much I can tell you here because this is rather 
cryptic.  It's illogical to get the same output with different input.  You can 
calculate exactly what values to use based on the number of residues in the 
protein (y-axis) and number of frames (x-axis).  Then scale xbox accordingly to 
fit some nicely shaped rectangle of defined proportions.

-Justin

>
>      On Sunday, February 14, 2016 5:05 PM, Justin Lemkul <jalem...@vt.edu> 
>wrote:
>
>
>
>
> On 2/14/16 1:54 AM, mohammad r wrote:
>> Thank you Justin,
>>
>> I used xpm2ps command with below m2p file but the resolution was not changed.
>> I've attached the xpm file, even the legend can't be seen.
>> is there anyway to get the result file in pdf format?
>>
>> m2p file (I found it in the gromacs website):
>>
>
>> xbox = 2.0 ; x‐size of a matrix element
>> ybox = 2.0 ; y‐size of a matrix element
>
> You have a rectangular matrix, with the x-dimension being much longer than the
> y-dimension.  If you set these two values to be the same, what happens to the
> size of the rectangle?  It gets uniformly scaled.  So naturally that
> accomplishes nothing.  What you need to do is reduce the ratio of xbox/ybox.
>
> -Justin
>

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] converted topology from amber to gromacs

[mohammad r]

Hi gromacs users,
I've generatedinitial structure of my system by using ambertools (topology 
andcoordinate files) and converted it to gromacs format (.gro and .top)by 
parmed, but in topology file it doesn't refer to any forcefield.Does it make 
any problem in the results or it is ok? Because when Icompare the simulation 
result with experiment it is incorrect.
Thank you, Mohammad.
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Re: [gmx-users] converted topology from amber to gromacs

[mohammad r]

Thank you very much Justin 

On Saturday, February 20, 2016 10:53 PM, Justin Lemkul <jalem...@vt.edu> 
wrote:
 

 

On 2/20/16 8:49 AM, mohammad r wrote:
> Hi Justin,
>
> Thank you for your answer, I used grompp and it didn't give me error. I've
> attached a topology file of my systems. Can you please take a look at this and
> tell me your opinion? You mean that it doesn't make any problem when after
> conversion process the topology file doesn't refer to any force field?
>

The topology lists all needed parameters explicitly.  Note the header that says 
"This is a standalone topology."  "Standalone" means "I have everything you 
need 
right here."

The purpose of the #include function in GROMACS is to say "copy and paste the 
contents of the file here."  That is the same thing for grompp as listing all 
parameters explicitly.

There is no problem here with your topology.  It just looks a little different, 
but if you understand a little bit about how GROMACS assembles topologies, it 
becomes obvious that this is a slightly more verbose version of what you are 
used to seeing.

-Justin

> Thank you, Mohammad.
>
>
>
>
> On Friday, February 19, 2016 4:38 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
>
>
> On 2/19/16 3:26 AM, mohammad r wrote:
>  >
>  > I don't know whether the problem is with the converting process (gromacs
> topology file doesn't refer to any force filed) or the the process of 
> generating
> files in amber tools is wrong.
>  >
>
> Are you getting some specific problem in GROMACS?  ParmEd should give you a
> self-contained topology file that explicitly lists the parameters it uses.  It
> may not fit the convention of the normal sequence of #include statements 
> because
> it's using a slightly different, but equally valid, approach.
>
> Without seeing your topology, it's impossible to figure out if there is any
> problem.  grompp is the quickest test here.  If it doesn't complain, you're 
> fine.
>
> -Justin
>
>  >      On Friday, February 19, 2016 11:04 AM, mohammad r
> <mohammad.r0...@yahoo.com <mailto:mohammad.r0...@yahoo.com>> wrote:
>  >
>  >
>  >  #yiv7024757511 p
> {margin-bottom:0.1in;direction:ltr;line-height:120%;text-align:justify;}#yiv7024757511
> p.yiv7024757511western {font-size:12pt;}#yiv7024757511 p.yiv7024757511cjk
> {font-size:12pt;}#yiv7024757511 p.yiv7024757511ctl {font-size:12pt;}I used
> ff14SBAmber protein force field, #yiv7024757511 p
> {margin-bottom:0.1in;direction:ltr;line-height:120%;text-align:justify;}#yiv7024757511
> p.yiv7024757511western {font-size:12pt;}#yiv7024757511 p.yiv7024757511cjk
> {font-size:12pt;}#yiv7024757511 p.yiv7024757511ctl {font-size:12pt;}
> LIPID11force field and TIP3P water model. First I  loaded the force fields and
> water model then loaded the pdb file and finally I saved the topology and
> coordinate files.
>
>  >
>  >
>  >      On Friday, February 19, 2016 10:40 AM, Hai Nguyen <nhai...@gmail.com
> <mailto:nhai...@gmail.com>> wrote:
>  >
>  >
>  >  Hi
>  > You should know which AMBER force field when you made the topology file. 
>(How
> did you make it?)
>  > Hai
>  > On Fri, Feb 19, 2016 at 12:56 AM, mohammad r <mohammad.r0...@yahoo.com
> <mailto:mohammad.r0...@yahoo.com>> wrote:
>  >
>  > Hi gromacs users,
>  > I've generatedinitial structure of my system by using ambertools (topology
> andcoordinate files) and converted it to gromacs format (.gro and .top)by
> parmed, but in topology file it doesn't refer to any forcefield.Does it make 
> any
> problem in the results or it is ok? Because when Icompare the simulation 
> result
> with experiment it is incorrect.
>  > Thank you, Mohammad.
>  > --
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>  > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
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>  >
>  >
>  >
>  >
>  >
>  >
>  >
>  >
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Healt

[gmx-users] Potential energy

[mohammad r]

Hi everybody,


 
Is it correct to say the potential energy after energyminimization should be 
negative and in the order of 105-106 ?according to gromacs tutorial:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html


Thank you, Mohammad.
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Re: [gmx-users] Potential energy

[mohammad r]

Thank you Justin,
do you know how I can find or modify the center of mass velocity of my system? 

On Sunday, February 21, 2016 11:50 PM, Justin Lemkul <jalem...@vt.edu> 
wrote:
 

 

On 2/21/16 3:15 PM, mohammad r wrote:
> Hi everybody,
>
>
>
> Is it correct to say the potential energy after energyminimization should be 
> negative and in the order of 105-106 ?according to gromacs tutorial:
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html
>

As a broad generalization, but strictly speaking, that's not always true.  A 
comparable protein in a similarly sized box will probably have something on 
that 
order, but that is by no means an absolute rule.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] DSSP secondary structure

[mohammad r]

Thank you Justin,
I used xpm2ps command with below m2p file but the resolution was not changed. 
I've attached the xpm file, even the legend can't be seen.is there anyway to 
get the result file in pdf format?
m2p file (I found it in the gromacs website):
black = no ; Obsoletetitlefont = Times‐Roman ; A PostScript 
Fonttitlefontsize = 20 ; Font size (pt)legend = yes ; Show the legendlegendfont 
= Times‐Roman ; A PostScript Fontlegendlabel = ; Used when there is none in the 
.xpmlegend2label = ; Used when merging two xpm'slegendfontsize = 14 ; Font size 
(pt)xbox = 2.0 ; x‐size of a matrix elementybox = 2.0 ; y‐size of a matrix 
elementmatrixspacing = 20.0 ; Space between 2 matricesxoffset = 0.0 ; Between 
matrix and bounding boxyoffset = 0.0 ; Between matrix and bounding boxx‐major = 
20 ; Major ticks on x axis every .. framesx‐minor = 5 ; Id. Minor 
ticksx‐firstmajor = 0 ; First frame for major tickx‐majorat0 = no ; Major tick 
at first framex‐majorticklen = 8.0 ; x‐majorticklengthx‐minorticklen = 4.0 ; 
x‐minorticklengthx‐label = ; Used when there is none in the .xpmx‐fontsize = 16 
; Font size (pt)x‐font = Times‐Roman ; A PostScript Fontx‐tickfontsize = 10 ; 
Font size (pt)x‐tickfont = Helvetica ; A PostScript Fonty‐major = 20y‐minor = 
5y‐firstmajor = 0y‐majorat0 = noy‐majorticklen = 8.0y‐minorticklen = 4.0y‐label 
=y‐fontsize = 16y‐font = Times‐Romany‐tickfontsize = 10y‐tickfont = Helvetica
 

On Saturday, February 13, 2016 9:44 PM, Justin Lemkul <jalem...@vt.edu> 
wrote:
 

 

On 2/13/16 1:33 AM, mohammad r wrote:
> Hi,
> I used the "gmx do_dssp" command to get the secondary structure of the 
> protein during the simulation but the resolution of the resulted .xpm file is 
> very low. how can I increase its resolution?

You can adjust the matrix proportions with an .m2p file passed to xpm2ps -di. 
These are almost always necessary as there are many more frames than residues 
in 
the protein, usually an order of magnitude or more.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==


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[gmx-users] modeling CNT, center of mass velocity, energy minimization

[mohammad r]

Hi GROMACS users,


 
I have some questions:


 
1-  Can I model a carbonnanotube (CNT) conveying fluid in GROMACS 
subjected to a magnetic field?

2-  How can I check the centerof mass velocity of my system?

3-  I want to calculate volumeand water self diffusion coefficient for 
1ns, can the energy minimizationprocess do it? Or the equilibrium processes can 
do it? I want to draw theparameters versus time.


 
Thank you, Mohammad.

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Re: [gmx-users] Neutralizing

[mohammad r]

Thank you Justin for your help. 

On Wednesday, March 9, 2016 6:38 PM, Justin Lemkul <jalem...@vt.edu> wrote:
 

 

On 3/9/16 1:42 AM, mohammad r wrote:
> Thank you Parham and Justin, Excuse me I have another question, in simulation
> of a water-peptide system, is it necessary to use QM/MM simulation during the
> entire process? Because I didn't see it in the tutorials. By the way I
> generated the pdb file by using charmm-gui then import it in amber to get the
> topology and coordinate files, finally I converted the topology and
> coordinate files to gromacs format and did the rest of simulation by gromacs.
> but I didn't run QM/MM simulation. Does it make trouble in the results?

The technique(s) used depend on the scientific question(s) being posed before 
doing the simulations.  If you expect some reactions, etc. to be taking place, 
then you need QM/MM.  If you just want to simulate a peptide over time, then 
plain MD is fine.  Methodological details like this should be decided long 
before one approaches a keyboard :)

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==


  
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Re: [gmx-users] Neutralizing

[mohammad r]

Thank you Parham and Justin,
Excuse me I have another question, in simulation of a water-peptide system, is 
it necessary to use QM/MM simulation during the entire process? Because I 
didn't see it in the tutorials. By the way I generated the pdb file by using 
charmm-gui then import it in amber to get the topology and coordinate files, 
finally I converted the topology and coordinate files to gromacs format and did 
the rest of simulation by gromacs. but I didn't run QM/MM simulation. Does it 
make trouble in the results?
Best, Mohammad. 

On Wednesday, March 9, 2016 4:26 AM, Justin Lemkul <jalem...@vt.edu> wrote:
 

 

On 3/8/16 3:59 AM, mohammad r wrote:
> Thank you Parham
> You mean that it is not necessary to do QM/MM simulation?
>

The trivial task of adding ions to neutralize the net charge on the system 
certainly does not require anything like QM/MM.

-Justin

>      On Tuesday, March 8, 2016 11:13 AM, Parham Jabbarzadeh (Department of 
>Biomedical Science) <pjabbarza...@gmail.com> wrote:
>
>
>  Dear Sir
>
> Use this command:
>
> gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -neutral
>
> In this case, you don't need ​the number of ions​.
> Kind Regards
>
> Parham J. K.
> ​​==​==​=
> ​PhD candidate - Lecturer in drug discovery
> Faculty of Medicine and Health SciencesUniversity Putra MalaysiaMalaysia
> ​==​===Publication ::: Featured Publication ::: Website 
> ::: FaceBook
> On Tue, Mar 8, 2016 at 3:32 PM, mohammad r <mohammad.r0...@yahoo.com> wrote:
>
> Hi everybody, I’ve generated a water-peptide system, now I want to neutralize 
> it. Is adding adequate number of ions sufficient for neutralizing process or 
> I should do QM/MM simulation for the this process? Thank you, Mohammad.
> --
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>
>

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] QM calculation

[mohammad r]

Thank you Justin, I want to do QM calculationbefore running equilibration then 
run the MD simulation by GROMACS. Do you knowwhich software is appropriate and 
compatible with GROMACS that after QM calculation I can run the rest of 
simulation?
Best, Mohammad.

On Thursday, March 31, 2016 3:43 AM, Justin Lemkul <jalem...@vt.edu> wrote:
 

 

On 3/30/16 2:17 AM, mohammad r wrote:
> Hi gromacs users,
>
>
>
> I want to do QMcalculation to my system. Can the PRODRG sitedo it (according
> to gromacs tutorial)? Or I should do it by using gromacsitself? By the way

QM calculations are not reliant on MM topologies, like those from PRODRG (which 
are poor quality anyway) or any force field terms.

GROMACS does not do QM directly, though there are interfaces to popular QM 
codes 
for doing QM/MM.  For strict QM, abandon GROMACS and use the appropriate 
software.

> I’ve generated the initial coordinate and topology files inamber tools then
> convert it to gromacs format by using parmed (because theforce field which I
> want is not included in gromacs).
>

Again, for a pure QM calculation, there is no need for any MM programs or force 
fields.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Run mdrun in parallel

[Husen R]

Hi all,

Currently, I'm trying to run mdrun command in parallel.
the following is my batch script using Slurm as a resource manager:

=Batch Script==
#!/bin/bash
#SBATCH -J Eq1
#SBATCH -o eq1-%j.out
#SBATCH -A pro
#SBATCH -N 2
#SBATCH -n 16

gmx mdrun -deffnm tpr
===End Batch Script===

As we can see from the batch script above, I tried to run mdrun with 2
Nodes and 16 processors.
After the batch job is submitted, I tried to see running process in the
background in each node using htop command and I found that only one node
that run 'gmx mdrun -deffnm tpr' command, there was no running process
called 'gmx mdrun -deffnm tpr' in the other one.

Please, anyone tell me how to run mdrun (or gromacs in general) in parallel
?

note : If I run mpi application, I always able to see it running in every
allocated nodes using htop.

thank you in advance.

Regards,


Husen
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Re: [gmx-users] Gromacs 5.1.2 installation problem

[Husen R]

Hello James,

Thank you for your reply and valuable information.

I tried running "gmx [command]" and it works.
Sorry for this fundamental question.

Regards,

Husen

On Tue, Apr 5, 2016 at 4:11 PM, James Graham <j.a.gra...@soton.ac.uk> wrote:

> Hi Husen,
>
> In GROMACS version 5.1 the default program naming scheme was changed so
> that everything is now part of the executable 'gmx'.  Because of this you
> need to use 'gmx pdb2gmx' (and e.g. 'gmx grompp', 'gmx mdrun') instead.
>
> The change was actually made in version 5.0, but they left an option to
> use it the old way as well.
>
> Regards,
> James
>
>
> On 05/04/16 08:19, Husen R wrote:
>
>> Dear all,
>>
>> I already installed gromacs-5.1.2 succesfully with the following
>> instruction :
>>
>> tar xfz gromacs-5.1.2.tar.gz
>> cd gromacs-5.1.2
>> mkdir build
>> cd build
>> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON
>> make
>> make check
>> sudo make install
>> source /usr/local/gromacs/bin/GMXRC
>>
>> However, after finishing installation I can not use mdrun, pdb2gmx
>> (and possibly other commands).
>> The following is the error message when I tried to run pdb2gmx command.
>>
>> The program 'pdb2gmx' is currently not installed. You can install it by
>> typing:
>> sudo apt-get install gromacs
>>
>> I tried to find those commands using "locate" command but they're
>> doesn't exist as if gromacs is not installed.
>> Note : The installation directory /usr/local/gromacs is exist.
>>
>> anyone please tell me what will be the cause of this problem ?
>>
>> Regards,
>>
>>
>> Husen
>>
>
> --
> James Graham - PhD Student
> Institute for Complex Systems Simulation (ICSS)
> Computational Systems Chemistry
> University of Southampton, UK
>
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Re: [gmx-users] Neutralizing

[mohammad r]

Thank you Parham 
You mean that it is not necessary to do QM/MM simulation?

On Tuesday, March 8, 2016 11:13 AM, Parham Jabbarzadeh (Department of 
Biomedical Science) <pjabbarza...@gmail.com> wrote:
 

 Dear Sir

Use this command:

gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -neutral

In this case, you don't need ​the number of ions​.
Kind Regards

Parham J. K.
​​==​==​=
​PhD candidate - Lecturer in drug discovery
Faculty of Medicine and Health SciencesUniversity Putra MalaysiaMalaysia
​==​===Publication ::: Featured Publication ::: Website ::: 
FaceBook 
On Tue, Mar 8, 2016 at 3:32 PM, mohammad r <mohammad.r0...@yahoo.com> wrote:

Hi everybody, I’ve generated a water-peptide system, now I want to neutralize 
it. Is adding adequate number of ions sufficient for neutralizing process or I 
should do QM/MM simulation for the this process? Thank you, Mohammad.
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[gmx-users] Neutralizing

[mohammad r]

Hi everybody, I’ve generated a water-peptide system, now I want to neutralize 
it. Is adding adequate number of ions sufficient for neutralizing process or I 
should do QM/MM simulation for the this process? Thank you, Mohammad.
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[gmx-users] Gromacs 5.1.2 installation problem

[Husen R]

Dear all,

I already installed gromacs-5.1.2 succesfully with the following
instruction :

tar xfz gromacs-5.1.2.tar.gz
cd gromacs-5.1.2
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC

However, after finishing installation I can not use mdrun, pdb2gmx
(and possibly other commands).
The following is the error message when I tried to run pdb2gmx command.

The program 'pdb2gmx' is currently not installed. You can install it by typing:
sudo apt-get install gromacs

I tried to find those commands using "locate" command but they're
doesn't exist as if gromacs is not installed.
Note : The installation directory /usr/local/gromacs is exist.

anyone please tell me what will be the cause of this problem ?

Regards,


Husen
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Re: [gmx-users] QM calculation

[mohammad r]

Thank you very much Justin for your helpful answer. 

On Thursday, March 31, 2016 3:40 PM, Justin Lemkul <jalem...@vt.edu> wrote:
 

 

On 3/31/16 12:19 AM, mohammad r wrote:
> Thank you Justin, I want to do QM calculationbefore running equilibration
> then run the MD simulation by GROMACS. Do you knowwhich software is
> appropriate and compatible with GROMACS that after QM calculation I can run
> the rest of simulation?

Again, for a pure QM calculation (geometry optimization, I presume) there is no 
interaction with GROMACS or any other software.  You do your optimization, 
output the coordinates, and then move on.  If I'm missing some critical detail, 
please describe exactly what you want to do.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==


  
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[gmx-users] QM calculation

[mohammad r]

Hi gromacs users,


 
I want to do QMcalculation to my system. Can the PRODRG sitedo it (according to 
gromacs tutorial)? Or I should do it by using gromacsitself? By the way I’ve 
generated the initial coordinate and topology files inamber tools then convert 
it to gromacs format by using parmed (because theforce field which I want is 
not included in gromacs).


 
Thank you, Mohammad.

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Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example

[Husen R]

Hi,

Thanks a lot !
I'll try it,..

Regards,


Husen

On Sun, Apr 24, 2016 at 6:54 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 4/24/16 12:04 AM, Husen R wrote:
>
>> Dear all,
>>
>> is there any complete documentation discussing checkpoint/restart in
>> Gromacs-5.1.2 ?
>> I found this link that discuss checkpoint (
>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations) and
>> this link that discuss restart (
>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts) but these
>> are
>> not specifically for gromacs 5.1.2.
>>
>>
> There are no differences for 5.1.2, so that information is all relevant.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example

[Husen R]

Hi,


Thanks for your reply.

There is no state.cpt or state_prev.cpt file.

In equilibration part 1 the resulting checkpoint files : nvt.cpt and
nvt_prev.cpt
In equilibration part 2 the resulting checkpoint files : npt.cpt and
npt_prev.cpt
In Production MD the resulting checkpoint files  : md_0_1.cpt and
md_0_1_prev.cpt

is this because of -deffnm option ?
I just want to make sure.

Regards,


Husen


On Tue, Apr 26, 2016 at 11:45 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> On Tue, 26 Apr 2016 06:19 Husen R <hus...@gmail.com> wrote:
>
> > Hi all,
> >
> > I tried to run this gromacs tutorial (
> >
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html
> > )
> > in order to understand how checkpoint/restart works in Gromacs-5.1.2.
> >
> > Based on running that tutorial I found that mdrun automatically
> checkpoint
> > even though I didn't specify -cpt option (based on mdrun manual page, by
> > default checkpoint every 15 minutes)
> >
>
> Yes, as that webpage suggests.
>
> 1. What if I specify -cpt option with a value longer than or smaller than
> > 15 minutes ? does -cpt value will automatically override the default ?
> >
>
> Yes, the default is used when you don't supply a value. But usually you
> don't need to think about this.
>
> 2. I run the following command to restart production MD step (using SLURM)
> > from checkpoint file. md_0_1_prev.cpt is .cpt file resulting from
> previous
> > mdrun execution. is my command right ? I just want to make sure.
> >
>
> Not quite. From that webpage: "Note that mdrun will write state.cpt and
> state_prev.cpt files. As you can see from their time stamps, one was
> written approximately at the checkpoint interval before the other (15 mins
> by default). Or you can use gmxcheck to see what is in them." You want to
> follow the examples there and do your restart from the most recent file,
> which is state.cpt. The older file is just kept for safety. Your command
> will lead to wasting 15 minutes of simulation.
>
> Mark
>
> #!/bin/bash
> > #SBATCH -J Lysozyme
> > #SBATCH -o md-%j.out
> > #SBATCH -A necis
> > #SBATCH -N 3
> > #SBATCH -n 24
> > #SBATCH --time=144:00:00
> > #SBATCH --mail-user=hus...@gmail.com
> > #SBATCH --mail-type=begin
> > #SBATCH --mail-type=end
> >
> > mpirun gmx_mpi mdrun -cpi md_0_1_prev.cpt -deffnm md_0_1
> >
> >
> > Thank you in advance
> >
> > Regards,
> >
> >
> > Husen
> >
> >
> > On Sun, Apr 24, 2016 at 7:57 PM, Husen R <hus...@gmail.com> wrote:
> >
> > > Hi,
> > >
> > > Thanks a lot !
> > > I'll try it,..
> > >
> > > Regards,
> > >
> > >
> > > Husen
> > >
> > > On Sun, Apr 24, 2016 at 6:54 PM, Justin Lemkul <jalem...@vt.edu>
> wrote:
> > >
> > >>
> > >>
> > >> On 4/24/16 12:04 AM, Husen R wrote:
> > >>
> > >>> Dear all,
> > >>>
> > >>> is there any complete documentation discussing checkpoint/restart in
> > >>> Gromacs-5.1.2 ?
> > >>> I found this link that discuss checkpoint (
> > >>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations)
> > and
> > >>> this link that discuss restart (
> > >>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts) but
> these
> > >>> are
> > >>> not specifically for gromacs 5.1.2.
> > >>>
> > >>>
> > >> There are no differences for 5.1.2, so that information is all
> relevant.
> > >>
> > >> -Justin
> > >>
> > >> --
> > >> ==
> > >>
> > >> Justin A. Lemkul, Ph.D.
> > >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >>
> > >> Department of Pharmaceutical Sciences
> > >> School of Pharmacy
> > >> Health Sciences Facility II, Room 629
> > >> University of Maryland, Baltimore
> > >> 20 Penn St.
> > >> Baltimore, MD 21201
> > >>
> > >> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > >> http://mackerell.umaryland.edu/~jalemkul
> > >>
> > >> ==
> > >> --
> > >> Gromacs Users mailing list
> > >>
> > >> * Please search the archive at
&

Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example

[Husen R]

Hi all,

I tried to run this gromacs tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html)
in order to understand how checkpoint/restart works in Gromacs-5.1.2.

Based on running that tutorial I found that mdrun automatically checkpoint
even though I didn't specify -cpt option (based on mdrun manual page, by
default checkpoint every 15 minutes)

1. What if I specify -cpt option with a value longer than or smaller than
15 minutes ? does -cpt value will automatically override the default ?

2. I run the following command to restart production MD step (using SLURM)
from checkpoint file. md_0_1_prev.cpt is .cpt file resulting from previous
mdrun execution. is my command right ? I just want to make sure.

#!/bin/bash
#SBATCH -J Lysozyme
#SBATCH -o md-%j.out
#SBATCH -A necis
#SBATCH -N 3
#SBATCH -n 24
#SBATCH --time=144:00:00
#SBATCH --mail-user=hus...@gmail.com
#SBATCH --mail-type=begin
#SBATCH --mail-type=end

mpirun gmx_mpi mdrun -cpi md_0_1_prev.cpt -deffnm md_0_1


Thank you in advance

Regards,


Husen


On Sun, Apr 24, 2016 at 7:57 PM, Husen R <hus...@gmail.com> wrote:

> Hi,
>
> Thanks a lot !
> I'll try it,..
>
> Regards,
>
>
> Husen
>
> On Sun, Apr 24, 2016 at 6:54 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>>
>>
>> On 4/24/16 12:04 AM, Husen R wrote:
>>
>>> Dear all,
>>>
>>> is there any complete documentation discussing checkpoint/restart in
>>> Gromacs-5.1.2 ?
>>> I found this link that discuss checkpoint (
>>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations) and
>>> this link that discuss restart (
>>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts) but these
>>> are
>>> not specifically for gromacs 5.1.2.
>>>
>>>
>> There are no differences for 5.1.2, so that information is all relevant.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
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[gmx-users] Gromacs-5.1.2 Checkpoint/restart example

[Husen R]

Dear all,

is there any complete documentation discussing checkpoint/restart in
Gromacs-5.1.2 ?
I found this link that discuss checkpoint (
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations) and
this link that discuss restart (
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts) but these are
not specifically for gromacs 5.1.2.

Thank you in advance.

Regards,



Husen
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[gmx-users] Adding ions

[mohammad r]

 Hi GROMACS users,
I solved my proteinin a defined box of water. Now I want to add ions to 
neutralize thesystem. But when I use “grompp -f ions.mdp -c solv.gro 
-pgromacs.top -o ions.tpr” to generate the .tpr file I receive thiserror :
Fatal error:No such moleculetypeSOLFor more informationand tips for 
troubleshooting, please check the GROMACSwebsite 
athttp://www.gromacs.org/Documentation/Errors
in the .gro and .topboth the SOL exists. I don not know what the problem is 
exactly.Also, before thiscommand I defined the box and solved the proteins by 
these commands: 
gmx editconf -fgromacs.gro -o protein.gro -c -box 8gmx solvate -cpprotein.gro 
-cs spc216.gro -o solv.gro -p gromacs.top
Thank you, Mohammad.
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Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

[Husen R]

Hi all,

After spending time for troubleshooting, I found that gromacs
checkpoint/restart feature is working well.

The failure occurred because I use root user to submit restart job (using
slurm resource manager). After switching to non root user, the restart
process is running.
The reason why I use root user is because I run this job in bash scripting
and execute it at designated time using Cron.
I know this is not the right place to talk about slurm.

Thank you for your reply !

Regards,

Husen

On Sun, May 15, 2016 at 8:20 PM, <jkrie...@mrc-lmb.cam.ac.uk> wrote:

> ok thanks
>
> > Hi,
> >
> > Yes, that's one way to work around the problem. In some places, a module
> > subsystem can be used to take care of the selection automatically, but
> you
> > don't want to set one up for just you to use.
> >
> > Mark
> >
> > On Sun, May 15, 2016 at 11:48 AM <jkrie...@mrc-lmb.cam.ac.uk> wrote:
> >
> >> Thanks Mark,
> >>
> >> My sysadmins have let me install my own GROMACS versions and have not
> >> informed me of any such mechanism. Would you suggest I qrsh into a node
> >> of
> >> each type and build an mdrun-only version on each? I'd then select a
> >> particular node type for a submit script with the relevant mdrun.
> >>
> >> Many thanks
> >> James
> >>
> >> > Hi,
> >> >
> >> > On Sat, May 14, 2016 at 1:09 PM <jkrie...@mrc-lmb.cam.ac.uk> wrote:
> >> >
> >> >> In case it's relevant/interesting to anyone, here are the details on
> >> our
> >> >> cluster nodes:
> >> >>
> >> >> nodes   #   model   # cores cpu
> >> >> model
> >> >>   RAM   node_type
> >> >> fmb01 - fmb33   33  IBM HS21XM  8   3 GHz
> >> >> Xeon
> >> >> E5450
> >> >>  16GB   hs21
> >> >> fmb34 - fmb42   9   IBM HS228   2.4
> >> GHz
> >> >> Xeon E5530
> >> >> 16GBhs22
> >> >> fmb43 - fmb88   45  Dell PE M6108   2.4
> >> GHz
> >> >> Xeon E5530
> >> >>  16GB   m610
> >> >> fmb88 - fmb90   3   Dell PE M610+   12  3.4
> >> GHz
> >> >> Xeon X5690
> >> >>   48GB  m610+
> >> >> fmb91 - fmb202  112 Dell PE M62024 (HT) 2.9
> >> GHz
> >> >> Xeon E5-2667
> >> >>64GB m620
> >> >> fmb203 - fmb279 77  Dell PE M62024 (HT) 3.5
> >> GHz
> >> >> Xeon E5-2643 v2 64GB
> >> >> m620+
> >> >> fmb280 - fmb359 80  Dell PE M63024 (HT) 3.4
> >> GHz
> >> >> Xeon E5-2643 v3 64GB
> >> >> m630
> >> >>
> >> >> I could only run GROMACS 4.6.2 on the last three node types and I
> >> >> believe
> >> >> the same is true for 5.0.4
> >> >>
> >> >
> >> > Sure. GROMACS is designed to target whichever hardware was selected at
> >> > configure time, which your sysadmins for such a heterogeneous cluster
> >> > should have documented somewhere. They should also be making available
> >> to
> >> > you a mechanism to target your jobs to nodes where they can run
> >> programs
> >> > that use the hardware efficiently, or providing GROMACS installations
> >> that
> >> > work regardless of which node you are actually on. You might like to
> >> > respectfully remind them of the things we say at
> >> >
> >>
> http://manual.gromacs.org/documentation/5.1.2/install-guide/index.html#portability-aspects
> >> > (These thoughts are common to earlier versions also.)
> >> >
> >> > Mark
> >> >
> >> >
> >> > Best wishes
> >> >> James
> >> >>
> >> >> > I have found that only some kinds of nodes on our cluster work for
> >> >> gromacs
> >> >> > 4.6 (the ones we call m620, m620+ and m630 but not others - I can
> >> >> check
> >> >> > the details tomorrow). I haven't tested it again now I'm using 5.0
> >> so
> >> >> > don't know if that's still an issue but if it is it could explain
> >> why
> >&

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

[Husen R]

I use Gromacs-5.1.2 and SLURM-15.08.10 as a resource manager.

On Sat, May 14, 2016 at 7:53 AM, Husen R <hus...@gmail.com> wrote:

> Dear all
>
> Does simulation able to be restarted from checkpoint file with fewer nodes
> ?
> let's say, at the first time, I run simulation with 3 nodes. At running
> time, one of those nodes is crashed and the simulation is terminated.
>
> I want to restart that simulation immadiately based on checkpoint file
> with the remaining 2 nodes. does gromacs support such case ?
> I need help.
>
> Thank you in advance.
> Regards,
>
> Husen
>
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[gmx-users] Restart simulation from checkpoint file with fewer nodes

[Husen R]

Dear all

Does simulation able to be restarted from checkpoint file with fewer nodes ?
let's say, at the first time, I run simulation with 3 nodes. At running
time, one of those nodes is crashed and the simulation is terminated.

I want to restart that simulation immadiately based on checkpoint file with
the remaining 2 nodes. does gromacs support such case ?
I need help.

Thank you in advance.
Regards,

Husen
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Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

[Husen R]

thanks a lot for your fast response.

I have tried it, and it failed. I ask in this forum just to make sure.
However, there was something in my cluster that probably make it failed.
I'll handle it first and then retry to restart again.

Regards,

Husen

On Sat, May 14, 2016 at 7:58 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 5/13/16 8:53 PM, Husen R wrote:
>
>> Dear all
>>
>> Does simulation able to be restarted from checkpoint file with fewer
>> nodes ?
>> let's say, at the first time, I run simulation with 3 nodes. At running
>> time, one of those nodes is crashed and the simulation is terminated.
>>
>> I want to restart that simulation immadiately based on checkpoint file
>> with
>> the remaining 2 nodes. does gromacs support such case ?
>> I need help.
>>
>
> Have you tried it?  It should work.  You will probably get a note about
> the continuation not being exact due to a change in the number of cores,
> but the run should proceed fine.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

[Husen R]

Hi,

Currently I'm running this tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html)
to simulate restart with fewer nodes.
at restart, I changed the amount of nodes from 3 to 2 nodes.
I also changed the amount of processes from 24 to 16 processes.

While the application is running, I tried to see the output file.
This is the content of the output file :

#output file


Reading checkpoint file md_0_1.cpt generated: Sat May 14 13:10:25 2016

  #ranks mismatch,
current program: 16
checkpoint file: 24

  #PME-ranks mismatch,
current program: -1
checkpoint file: 6

GROMACS patchlevel, binary or parallel settings differ from previous run.
Continuation is exact, but not guaranteed to be binary identical.

Using 16 MPI processes
Using 1 OpenMP thread per MPI process

starting mdrun 'LYSOZYME in water'
50 steps,   1000.0 ps (continuing from step 54500,109.0 ps).



I got a mismatch note as described in the output file above. it is not a
problem, isn't it ?
I just want to make sure.

is it not allowed to use a different user when we restart simulation from
checkpoint file ?
Previously, I failed to restart simulation based on checkpoint file. I
guess, it is failed because I used a different user (Only a guess).
Thank you in advance.

regards,

Husen




On Sat, May 14, 2016 at 7:58 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 5/13/16 8:53 PM, Husen R wrote:
>
>> Dear all
>>
>> Does simulation able to be restarted from checkpoint file with fewer
>> nodes ?
>> let's say, at the first time, I run simulation with 3 nodes. At running
>> time, one of those nodes is crashed and the simulation is terminated.
>>
>> I want to restart that simulation immadiately based on checkpoint file
>> with
>> the remaining 2 nodes. does gromacs support such case ?
>> I need help.
>>
>
> Have you tried it?  It should work.  You will probably get a note about
> the continuation not being exact due to a change in the number of cores,
> but the run should proceed fine.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
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>
> * Please search the archive at
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> posting!
>
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>
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Re: [gmx-users] Getting Fatal Error while running simulation of Protein-Ligand complex, at the stage of generating nvt.gro

[REMYA R]

Yes sir, even though its not working


On Sun, Apr 17, 2016 at 9:41 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 4/17/16 11:35 AM, REMYA R wrote:
>
>> Dear sir,
>>
>> I am getting error  while running simulation of Protein-Ligand complex ,
>> usong GROMOS force field, spc water model  at the equilibration phase of
>> bevan lab tutorial for protein-ligand simulation, version 4.6.1 (
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/06_equil.html
>> )
>>
>> Here below I am pasting some information from em.log
>>   D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S
>>
>>   av. #atoms communicated per step for force:  2 x 48020.5
>>
>>
>>   R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
>>
>>   Computing: Nodes Number G-CyclesSeconds %
>> ---
>>   Domain decomp.15152   11.0102.4 4.9
>>   DD comm. load 15  10.0040.0 0.0
>>   Send X to PME 151250.0690.0 0.0
>>   Comm. coord.  151255.5531.2 2.5
>>   Neighbor search   15125   21.0884.6 9.4
>>   Force 15125   21.4124.6 9.6
>>   Wait + Comm. F15125   20.4744.4 9.2
>>   PME mesh   9125   19.9294.3 8.9
>>   Wait + Comm. X/F   9  31.4866.814.1
>>   Wait + Recv. PME F151251.5070.3 0.7
>>   Constraints   152491.0620.2 0.5
>>   Comm. energies151252.6440.6 1.2
>>   Rest  15  87.106   18.939.0
>> ---
>>   Total 24 223.343   48.4   100.0
>> ---
>> ---
>>   PME redist. X/F92504.9821.1 2.2
>>   PME spread/gather  92506.7901.5 3.0
>>   PME 3D-FFT 92505.9991.3 2.7
>>   PME solve  91252.1520.5 1.0
>> ---
>>
>> Parallel run - timing based on wallclock.
>>
>> NODE (s)   Real (s)  (%)
>> Time:  2.016  2.016100.0
>> (Mnbf/s)   (GFlops)   (steps/hour)
>> Performance:337.723 47.730   223242.7
>> Finished mdrun on node 0 Thu Apr 14 19:38:14 2016
>>
>> I am new user for this simulation, could you please help me to rectify
>> this
>> error.Below I am pasting the error message that I got,
>> *Fatal error:*
>> A charge group moved too far between two domain decomposition steps
>> This usually means that your system is not well equilibrated
>>
>>
> Have you tried Google?  This error comes up almost daily on this list...
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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> * Please search the archive at
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[gmx-users] Getting Fatal Error while running simulation of Protein-Ligand complex, at the stage of generating nvt.gro

[REMYA R]

Dear sir,

I am getting error  while running simulation of Protein-Ligand complex ,
usong GROMOS force field, spc water model  at the equilibration phase of
bevan lab tutorial for protein-ligand simulation, version 4.6.1 (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/06_equil.html
)

Here below I am pasting some information from em.log
 D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S

 av. #atoms communicated per step for force:  2 x 48020.5


 R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

 Computing: Nodes Number G-CyclesSeconds %
---
 Domain decomp.15152   11.0102.4 4.9
 DD comm. load 15  10.0040.0 0.0
 Send X to PME 151250.0690.0 0.0
 Comm. coord.  151255.5531.2 2.5
 Neighbor search   15125   21.0884.6 9.4
 Force 15125   21.4124.6 9.6
 Wait + Comm. F15125   20.4744.4 9.2
 PME mesh   9125   19.9294.3 8.9
 Wait + Comm. X/F   9  31.4866.814.1
 Wait + Recv. PME F151251.5070.3 0.7
 Constraints   152491.0620.2 0.5
 Comm. energies151252.6440.6 1.2
 Rest  15  87.106   18.939.0
---
 Total 24 223.343   48.4   100.0
---
---
 PME redist. X/F92504.9821.1 2.2
 PME spread/gather  92506.7901.5 3.0
 PME 3D-FFT 92505.9991.3 2.7
 PME solve  91252.1520.5 1.0
---

Parallel run - timing based on wallclock.

   NODE (s)   Real (s)  (%)
   Time:  2.016  2.016100.0
   (Mnbf/s)   (GFlops)   (steps/hour)
Performance:337.723 47.730   223242.7
Finished mdrun on node 0 Thu Apr 14 19:38:14 2016

I am new user for this simulation, could you please help me to rectify this
error.Below I am pasting the error message that I got,
*Fatal error:*
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated

Thank you in advance
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Re: [gmx-users] mdrun on multiple nodes

[Husen R]

Hi Mark,

I have configured gromacs with mpi support (using -DGMX_MPI=on):

tar xfz gromacs-5.1.2.tar.gz
cd gromacs-5.1.2
mkdir build
cd build
cmake .. -DGMX_MPI=on -DGMX_BUILD_OWN_FFTW=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC

Currently, I tried to use gmx_mpi (as you said) instead of gmx and it works !
Using htop command, I can see that Each node has 8 processes running
"gmx_mpi mdrun -cpt 15 -deffnm md_0_1".
I can not wait to see the results.
Thank a lot.

Regards,

Husen


On Wed, Apr 20, 2016 at 3:48 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Probably you haven't built gromacs with MPI support, else the name of the
> binary would be gmx_mpi. You can get that confirmed if you look further
> down the output .log files.
>
> Mark
>
> On Wed, 20 Apr 2016 10:09 Husen R <hus...@gmail.com> wrote:
>
> > Hi all,
> >
> > I tried to run mdrun on more than one node using the command available in
> > this url
> >
> >
> http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-performance.html
> > .
> > The following is my sbatch job :
> >
> > ###SBATCH
> > #!/bin/bash
> > #SBATCH -J sim
> > #SBATCH -o md-%j.out
> > #SBATCH -A pro
> > #SBATCH -N 3
> > #SBATCH -n 24
> > #SBATCH --time=144:00:00
> > #SBATCH --mail-user=hus...@gmail.com
> > #SBATCH --mail-type=begin
> > #SBATCH --mail-type=end
> >
> > mpirun gmx mdrun -cpt 15 -deffnm md_0_1
> >
> > #SBATCH END
> >
> > I open the output file to see the result. It contains something
> repeatedly
> > as shown below:
> >
> > #OUTPUT###
> > ..
> > ..
> > ..
> >*GROMACS is written by:*
> >  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
> > Bjelkmar
> >  Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian
> Fritsch
> >   Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent
> > Hindriksen
> >  Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten
> Kutzner
> >
> > Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter
> Meulenhoff
> >Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
> >Roland Schulz Alexey Shvetsov Michael Shirts  Executable:
> > /usr/local/gromacs/bin/gmx
> >Alfons Sijbers
> >Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
> >and the project leaders:
> > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
> >
> > Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> > Copyright (c) 2001-2015, The GROMACS development team at
> > Uppsala University, Stockholm University and
> > the Royal Institute of Technology, Sweden.
> > check out http://www.gromacs.org for more information.
> >
> > GROMACS is free software; you can redistribute it and/or modify it
> > under the terms of the GNU Lesser General Public License
> > as published by the Free Software Foundation; either version 2.1
> > Data prefix:  /usr/local/gromacs
> > Command line:
> >   gmx mdrun -cpt 15 -deffnm md_0_1
> >
> > of the License, or (at your option) any later version.
> >
> > GROMACS:  gmx mdrun, VERSION 5.1.2
> > Executable:   /usr/local/gromacs/bin/gmx
> > Data prefix:  /usr/local/gromacs
> > Command line:
> >   gmx mdrun -cpt 15 -deffnm md_0_1
> >
> >:-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:
> >
> >* GROMACS is written by:*
> >  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
> > Bjelkmar
> >  Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian
> Fritsch
> >   Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent
> > Hindriksen
> >  Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten
> Kutzner
> >
> > Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter
> Meulenhoff
> >Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
> >Roland Schulz Alexey Shvetsov Michael Shirts Alfons
> Sijbers
> >Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
> >and the project leaders:
> > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
> >
> > Copyright (c) 1991-2000, Univer

Re: [gmx-users] mdrun on multiple nodes

[Husen R]

Hi Mark,

I have configured gromacs with mpi support (using -DGMX_MPI=on):

tar xfz gromacs-5.1.2.tar.gz
cd gromacs-5.1.2
mkdir build
cd build
cmake .. -DGMX=on -DGMX_BUILD_OWN_FFTW=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC

Currently, I tried to use gmx_mpi (as you said) instead of gmx and it works !
Using htop command, I can see that Each node has 8 processes running
"gmx_mpi mdrun -cpt 15 -deffnm md_0_1".
I can not wait to see the results.
Thank a lot.

Regards,

Husen



On Wed, Apr 20, 2016 at 3:48 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Probably you haven't built gromacs with MPI support, else the name of the
> binary would be gmx_mpi. You can get that confirmed if you look further
> down the output .log files.
>
> Mark
>
> On Wed, 20 Apr 2016 10:09 Husen R <hus...@gmail.com> wrote:
>
> > Hi all,
> >
> > I tried to run mdrun on more than one node using the command available in
> > this url
> >
> >
> http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-performance.html
> > .
> > The following is my sbatch job :
> >
> > ###SBATCH
> > #!/bin/bash
> > #SBATCH -J sim
> > #SBATCH -o md-%j.out
> > #SBATCH -A pro
> > #SBATCH -N 3
> > #SBATCH -n 24
> > #SBATCH --time=144:00:00
> > #SBATCH --mail-user=hus...@gmail.com
> > #SBATCH --mail-type=begin
> > #SBATCH --mail-type=end
> >
> > mpirun gmx mdrun -cpt 15 -deffnm md_0_1
> >
> > #SBATCH END
> >
> > I open the output file to see the result. It contains something
> repeatedly
> > as shown below:
> >
> > #OUTPUT###
> > ..
> > ..
> > ..
> >*GROMACS is written by:*
> >  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
> > Bjelkmar
> >  Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian
> Fritsch
> >   Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent
> > Hindriksen
> >  Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten
> Kutzner
> >
> > Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter
> Meulenhoff
> >Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
> >Roland Schulz Alexey Shvetsov Michael Shirts  Executable:
> > /usr/local/gromacs/bin/gmx
> >Alfons Sijbers
> >Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
> >and the project leaders:
> > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
> >
> > Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> > Copyright (c) 2001-2015, The GROMACS development team at
> > Uppsala University, Stockholm University and
> > the Royal Institute of Technology, Sweden.
> > check out http://www.gromacs.org for more information.
> >
> > GROMACS is free software; you can redistribute it and/or modify it
> > under the terms of the GNU Lesser General Public License
> > as published by the Free Software Foundation; either version 2.1
> > Data prefix:  /usr/local/gromacs
> > Command line:
> >   gmx mdrun -cpt 15 -deffnm md_0_1
> >
> > of the License, or (at your option) any later version.
> >
> > GROMACS:  gmx mdrun, VERSION 5.1.2
> > Executable:   /usr/local/gromacs/bin/gmx
> > Data prefix:  /usr/local/gromacs
> > Command line:
> >   gmx mdrun -cpt 15 -deffnm md_0_1
> >
> >:-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:
> >
> >* GROMACS is written by:*
> >  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
> > Bjelkmar
> >  Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian
> Fritsch
> >   Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent
> > Hindriksen
> >  Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten
> Kutzner
> >
> > Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter
> Meulenhoff
> >Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
> >Roland Schulz Alexey Shvetsov Michael Shirts Alfons
> Sijbers
> >Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
> >and the project leaders:
> > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
> >
> > Copyright (c) 1991-2000, Univer

[gmx-users] mdrun on multiple nodes

[Husen R]

Hi all,

I tried to run mdrun on more than one node using the command available in
this url
http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-performance.html
.
The following is my sbatch job :

###SBATCH
#!/bin/bash
#SBATCH -J sim
#SBATCH -o md-%j.out
#SBATCH -A pro
#SBATCH -N 3
#SBATCH -n 24
#SBATCH --time=144:00:00
#SBATCH --mail-user=hus...@gmail.com
#SBATCH --mail-type=begin
#SBATCH --mail-type=end

mpirun gmx mdrun -cpt 15 -deffnm md_0_1

#SBATCH END

I open the output file to see the result. It contains something repeatedly
as shown below:

#OUTPUT###
..
..
..
   *GROMACS is written by:*
 Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
Bjelkmar
 Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch
  Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent Hindriksen
 Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten Kutzner

Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
   Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
   Roland Schulz Alexey Shvetsov Michael Shirts  Executable:
/usr/local/gromacs/bin/gmx
   Alfons Sijbers
   Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
   and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
Data prefix:  /usr/local/gromacs
Command line:
  gmx mdrun -cpt 15 -deffnm md_0_1

of the License, or (at your option) any later version.

GROMACS:  gmx mdrun, VERSION 5.1.2
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
  gmx mdrun -cpt 15 -deffnm md_0_1

   :-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:

   * GROMACS is written by:*
 Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
Bjelkmar
 Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch
  Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent Hindriksen
 Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten Kutzner

Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
   Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
   Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
   Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
   and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx mdrun, VERSION 5.1.2
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
  gmx mdrun -cpt 15 -deffnm md_0_1

..
..
..

OUTPUT END###

Is it normal for output file to have such content?

in addition, as we can see from my sbatch script, I use 3 nodes and 24
processes. Using that configuration, I hope each node will have 8 processes
running "gmx mdrun -cpt 15 -deffnm md_0_1".
However, when I see running processes in each node using htop command, each
node has more than 60 processes running "gmx mdrun -cpt 15 -deffnm md_0_1".
why is this happened ? I need help.

Thank you in advance.


regards,


Husen
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* Please search the archive at 
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Re: [gmx-users] mdrun on multiple nodes

[Husen R]

Hi Mark,

I'm wondering why in this link
http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-performance.html
'gmx' is used to run mdrun on more than one node instead of 'gmx_mpi' ?

Regards,

Husen

On Wed, Apr 20, 2016 at 3:48 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Probably you haven't built gromacs with MPI support, else the name of the
> binary would be gmx_mpi. You can get that confirmed if you look further
> down the output .log files.
>
> Mark
>
> On Wed, 20 Apr 2016 10:09 Husen R <hus...@gmail.com> wrote:
>
> > Hi all,
> >
> > I tried to run mdrun on more than one node using the command available in
> > this url
> >
> >
> http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-performance.html
> > .
> > The following is my sbatch job :
> >
> > ###SBATCH
> > #!/bin/bash
> > #SBATCH -J sim
> > #SBATCH -o md-%j.out
> > #SBATCH -A pro
> > #SBATCH -N 3
> > #SBATCH -n 24
> > #SBATCH --time=144:00:00
> > #SBATCH --mail-user=hus...@gmail.com
> > #SBATCH --mail-type=begin
> > #SBATCH --mail-type=end
> >
> > mpirun gmx mdrun -cpt 15 -deffnm md_0_1
> >
> > #SBATCH END
> >
> > I open the output file to see the result. It contains something
> repeatedly
> > as shown below:
> >
> > #OUTPUT###
> > ..
> > ..
> > ..
> >*GROMACS is written by:*
> >  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
> > Bjelkmar
> >  Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian
> Fritsch
> >   Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent
> > Hindriksen
> >  Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten
> Kutzner
> >
> > Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter
> Meulenhoff
> >Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
> >Roland Schulz Alexey Shvetsov Michael Shirts  Executable:
> > /usr/local/gromacs/bin/gmx
> >Alfons Sijbers
> >Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
> >and the project leaders:
> > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
> >
> > Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> > Copyright (c) 2001-2015, The GROMACS development team at
> > Uppsala University, Stockholm University and
> > the Royal Institute of Technology, Sweden.
> > check out http://www.gromacs.org for more information.
> >
> > GROMACS is free software; you can redistribute it and/or modify it
> > under the terms of the GNU Lesser General Public License
> > as published by the Free Software Foundation; either version 2.1
> > Data prefix:  /usr/local/gromacs
> > Command line:
> >   gmx mdrun -cpt 15 -deffnm md_0_1
> >
> > of the License, or (at your option) any later version.
> >
> > GROMACS:  gmx mdrun, VERSION 5.1.2
> > Executable:   /usr/local/gromacs/bin/gmx
> > Data prefix:  /usr/local/gromacs
> > Command line:
> >   gmx mdrun -cpt 15 -deffnm md_0_1
> >
> >:-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:
> >
> >* GROMACS is written by:*
> >  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
> > Bjelkmar
> >  Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian
> Fritsch
> >   Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent
> > Hindriksen
> >  Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten
> Kutzner
> >
> > Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter
> Meulenhoff
> >Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
> >Roland Schulz Alexey Shvetsov Michael Shirts Alfons
> Sijbers
> >Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
> >and the project leaders:
> > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
> >
> > Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> > Copyright (c) 2001-2015, The GROMACS development team at
> > Uppsala University, Stockholm University and
> > the Royal Institute of Technology, Sweden.
> > check out http://www.gromacs.org for more information.
> >
> > GROMACS is free 

Re: [gmx-users] mdrun on multiple nodes

[Husen R]

Hi,


Thank a lot for the information.

in my gromacs installation, 'gmx_mpi' is works while 'mdrun_mpi' is not
recognized as a gromacs command.

Regards,


Husen


On Wed, Apr 20, 2016 at 6:42 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Well spotted. These should all be along the lines of
>
> mpirun -np 2 gmx_mpi mdrun
>
> or
>
> mpirun -np 2 mdrun_mpi
>
> if the admins have done an mdrun-only installation.
>
> I'll fix that for future versions
>
> Mark
>
> On Wed, 20 Apr 2016 13:34 Husen R <hus...@gmail.com> wrote:
>
> > Hi Mark,
> >
> > I'm wondering why in this link
> >
> >
> http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-performance.html
> > 'gmx' is used to run mdrun on more than one node instead of 'gmx_mpi' ?
> >
> > Regards,
> >
> > Husen
> >
> > On Wed, Apr 20, 2016 at 3:48 PM, Mark Abraham <mark.j.abra...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > Probably you haven't built gromacs with MPI support, else the name of
> the
> > > binary would be gmx_mpi. You can get that confirmed if you look further
> > > down the output .log files.
> > >
> > > Mark
> > >
> > > On Wed, 20 Apr 2016 10:09 Husen R <hus...@gmail.com> wrote:
> > >
> > > > Hi all,
> > > >
> > > > I tried to run mdrun on more than one node using the command
> available
> > in
> > > > this url
> > > >
> > > >
> > >
> >
> http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-performance.html
> > > > .
> > > > The following is my sbatch job :
> > > >
> > > > ###SBATCH
> > > > #!/bin/bash
> > > > #SBATCH -J sim
> > > > #SBATCH -o md-%j.out
> > > > #SBATCH -A pro
> > > > #SBATCH -N 3
> > > > #SBATCH -n 24
> > > > #SBATCH --time=144:00:00
> > > > #SBATCH --mail-user=hus...@gmail.com
> > > > #SBATCH --mail-type=begin
> > > > #SBATCH --mail-type=end
> > > >
> > > > mpirun gmx mdrun -cpt 15 -deffnm md_0_1
> > > >
> > > > #SBATCH END
> > > >
> > > > I open the output file to see the result. It contains something
> > > repeatedly
> > > > as shown below:
> > > >
> > > > #OUTPUT###
> > > > ..
> > > > ..
> > > > ..
> > > >*GROMACS is written by:*
> > > >  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
> > > > Bjelkmar
> > > >  Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian
> > > Fritsch
> > > >   Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent
> > > > Hindriksen
> > > >  Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten
> > > Kutzner
> > > >
> > > > Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter
> > > Meulenhoff
> > > >Erik Marklund  Teemu Murtola   Szilard Pall   Sander
> > Pronk
> > > >Roland Schulz Alexey Shvetsov Michael Shirts  Executable:
> > > > /usr/local/gromacs/bin/gmx
> > > >Alfons Sijbers
> > > >Peter TielemanTeemu Virolainen  Christian WennbergMaarten
> > Wolf
> > > >and the project leaders:
> > > > Mark Abraham, Berk Hess, Erik Lindahl, and David van der
> Spoel
> > > >
> > > > Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> > > > Copyright (c) 2001-2015, The GROMACS development team at
> > > > Uppsala University, Stockholm University and
> > > > the Royal Institute of Technology, Sweden.
> > > > check out http://www.gromacs.org for more information.
> > > >
> > > > GROMACS is free software; you can redistribute it and/or modify it
> > > > under the terms of the GNU Lesser General Public License
> > > > as published by the Free Software Foundation; either version 2.1
> > > > Data prefix:  /usr/local/gromacs
> > > > Command line:
> > > >   gmx mdrun -cpt 15 -deffnm md_0_1
> > > >
> > > > of the License, or (at your option) any late

[gmx-users] gmx xpm2ps

[Kulkarni R]

Hi gromacs users,


After completing production run, I gave this command


gmx xpm2ps -f hbmap.xpm - o hbplot.eps -rainbow red


However, I got error,


---
Program: gmx xpm2ps, VERSION 5.1.1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
Function:void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
  In command-line option -f
File '-' does not exist or is not accessible.
The following extensions were tried to complete the file name:
  .xpm
  In command-line option -f
File 'o' does not exist or is not accessible.
The following extensions were tried to complete the file name:
  .xpm
  In command-line option -f
File name 'hbplot.eps' cannot be used for this option.
Only the following extensions are possible:
  .xpm


How to avoid this error?

What command should be given preceding to this?

How to get plot of XpixelMap file?


Thanks,

Kulkarni.R
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Re: [gmx-users] gmx xpm2ps

[Kulkarni R]

Thank you very much.



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul 
<jalem...@vt.edu>
Sent: Friday, March 31, 2017 4:52 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx xpm2ps



On 3/31/17 11:27 AM, Kulkarni R wrote:
> Hi gromacs users,
>
>
> After completing production run, I gave this command
>
>
> gmx xpm2ps -f hbmap.xpm - o hbplot.eps -rainbow red
>
>
> However, I got error,
>
>
> ---
> Program: gmx xpm2ps, VERSION 5.1.1
> Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
> Function:void gmx::CommandLineParser::parse(int*, char**)
>
> Error in user input:
> Invalid command-line options
>   In command-line option -f
> File '-' does not exist or is not accessible.
> The following extensions were tried to complete the file name:
>   .xpm
>   In command-line option -f
> File 'o' does not exist or is not accessible.
> The following extensions were tried to complete the file name:
>   .xpm
>   In command-line option -f
> File name 'hbplot.eps' cannot be used for this option.
> Only the following extensions are possible:
>   .xpm
>
>
> How to avoid this error?
>

Don't put a space between - and o in trying to specify the output file,
otherwise you get this incorrect parsing of the command.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
[http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]<http://mackerell.umaryland.edu/~jalemkul>

Justin A. Lemkul - MacKerell Lab<http://mackerell.umaryland.edu/~jalemkul>
mackerell.umaryland.edu
Welcome to my site! To learn more about me and the work I am doing, please use 
the navigation links above.



==
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Re: [gmx-users] gmx xpm2ps

[Kulkarni R]

Thank you very much



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Diogo Vila 
Viçosa <diogo.vic...@fc.ul.pt>
Sent: Friday, March 31, 2017 5:00 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx xpm2ps

"gmx xpm2ps -f hbmap.xpm - o hbplot.eps -rainbow red" -> "gmx xpm2ps -f
hbmap.xpm -o hbplot.eps -rainbow red"

You have a blanck space between the "-" and the "o".




On Fri, Mar 31, 2017 at 5:52 PM Kulkarni R <alumniphys...@hotmail.com>
wrote:

> Hi gromacs users,
>
>
> After completing production run, I gave this command
>
>
> gmx xpm2ps -f hbmap.xpm - o hbplot.eps -rainbow red
>
>
> However, I got error,
>
>
> ---
> Program: gmx xpm2ps, VERSION 5.1.1
> Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
> Function:void gmx::CommandLineParser::parse(int*, char**)
>
> Error in user input:
> Invalid command-line options
>   In command-line option -f
> File '-' does not exist or is not accessible.
> The following extensions were tried to complete the file name:
>   .xpm
>   In command-line option -f
> File 'o' does not exist or is not accessible.
> The following extensions were tried to complete the file name:
>   .xpm
>   In command-line option -f
> File name 'hbplot.eps' cannot be used for this option.
> Only the following extensions are possible:
>   .xpm
>
>
> How to avoid this error?
>
> What command should be given preceding to this?
>
> How to get plot of XpixelMap file?
>
>
> Thanks,
>
> Kulkarni.R
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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> posting!
>
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Re: [gmx-users] LINEAR INTERACTION ENERGY

[Kulkarni R]

Thanks.


You have mentioned "proper energy groups" in mdp file


Could you please say more about it?


Thanks,

Kulkarni.R


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Vytautas 
Rakeviius <vytautas1...@yahoo.com>
Sent: Thursday, March 16, 2017 10:29 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] LINEAR INTERACTION ENERGY

Basically you do two MD runs one with ligand in water other with ligand in 
protein. You must set proper energygrps in mdp file so you get 2 edr files from 
runs and in the end you use "gmx lie" 
(http://manual.gromacs.org/programs/gmx-lie.html) to compute difference between 
those two edr files.You might check this paper too:
gmx lie - GROMACS<http://manual.gromacs.org/programs/gmx-lie.html>
manual.gromacs.org
Synopsis gmx lie [-f [.edr>]] [-o [.xvg>]] [-nice ] [-b ] [-e ] [-dt ] [-[no]w] 
[-xvg ] [-Elj ] [-Eqq ] [-Clj ] [-Cqq ] [-ligand ]


Curr Comput Aided Drug Des. 2015;11(3):237-44.

On Thursday, March 16, 2017 12:15 PM, Kulkarni R 
<alumniphys...@hotmail.com> wrote:


 Hi gromacs users,

In order to calculate delta G (Gibbs free energy) for protein ligand binding, 
what are the steps to be followed in Linear interaction energy?


Are there any tutorials for the same?


Thanks,

Kulkarni.R
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Re: [gmx-users] COMMAND TO DISPLAY SIMULATION COMPLETION TIME

[Kulkarni R]

Thanks



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Nikhil Maroli 

Sent: Thursday, March 16, 2017 7:41 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] COMMAND TO DISPLAY SIMULATION COMPLETION TIME

gmx mdrun -v


-v is the flag to use for the above
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[gmx-users] LINEAR INTERACTION ENERGY

[Kulkarni R]

Hi gromacs users,

In order to calculate delta G (Gibbs free energy) for protein ligand binding, 
what are the steps to be followed in Linear interaction energy?


Are there any tutorials for the same?


Thanks,

Kulkarni.R
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[gmx-users] INTERPRETING THE ENERGY VALUES AFTER SIMULATIONS IN GROMACS

[Kulkarni R]

Hi gromacs users,

After protein ligand simulations, I want to do energy analysis.

How to interpret the following data properly? What books and papers should we 
refer?

Energy   AverageErr.Est.   RMSDTot-Drift
---
Coul-SR:Protein-MOL-12.45493.611.7667   -19.8497  (kJ/mol)
LJ-SR:Protein-MOL-103.5021.17.06959 6.6227  (kJ/mol)

What is the significance of total drift?

Can someone offer suggestions and help me to improve?

Thanks,
Kulkarni.R

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[gmx-users] g_mmpbsa

[Kulkarni R]

 Hi gromacs users,

How to install mmpbsa using cgywin?

I am using gromacs through cgywin.

Thanks,
Kulkarni.R
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[gmx-users] Clayff forcefield

[G R]

 I try to implement CLYFF in gromacs. I created ffbonded.itp,
ffnonbonded.itp, atomtype.atp, forcefield.doc, forcefield.itp and
molecule.rtp. I want  to simulate Kaolinite, and I try to use pdb2gmx to
create a topology. My first question is that should I create any other
files? second, In molecule.rtp, I just write the atom type, atom name
and
charges. should I add bonds for each atom? Also, in rtp file, I don't
know
what should I write as a residue?
Thank you in advance,
Golnaz
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[gmx-users] Could not find clayff forcefield

[G R]

Dear users,

I try to implement Clayff forcefield for Kaolinite. I created my force
field (I'm not sure about it), but gromacs couldn't find my force field in
the directory. Here is my forcefield.

ffnonbonded
[ atomtypes ]
; name   mass  chargeptype  sigma  eps
 HW   1  1.00800 0.4100A0.0e-01  0.0e-01
;clayFF_waterhydrogen
 HO   1  1.00800 0.4250A0.0e-01  0.0e-01
;clayFF_hydroxylhydrogen
 OW   8 15.99800-0.8200A3.16557e-01  6.50209e-01
;ClayFF_wateroxygen
 OH   8 15.99800-0.9500A3.16557e-01  6.50209e-01
;ClayFF_hydroxyloxygen
 OB   8 15.99800-1.0500A3.16557e-01  6.50209e-01
;ClayFF_bridgingoxygen
 OBOS 8 15.99800-1.1808A3.16557e-01  6.50209e-01
;ClayFF_bridgingoxygenoctasub
 OBTS 8 15.99800-1.1688A3.16557e-01  6.50209e-01
;ClayFF_bridgingoxygentetrsub
 OHS  8 15.99800-1.0808A3.16557e-01  6.50209e-01
;ClayFF_hydroxyloxygensub
 SI  14 28.08600 2.1000A3.30208e-01  8.0e-06
;ClayFF_tetrahedralsilicon
 AO  13 26.98200 1.5750A4.27128e-01  6.0e-06
;ClayFF_octahedalaluminium
 AT  13 26.98200 1.5750A3.30206e-01  8.0e-06
;ClayFF_tetrasubaluminium

ffbonded
[ bondtypes ]
; ij  func   b0  kb
 OW HW   10.1000 554134.9
 OH HO   10.1000 554134.9
 OHSHO   10.1000 554134.9

[ angletypes ]
;  ijk  func   th0   cth
 HW   OWHW1109.47191.564
 AL   OHHO1109.47125.52

atomtype.n2t
HHW0.4100 1.008  1O  0.100 ;water hydrogen
OOW   -0.820015.998  2H  0.100H  0.100 ;water oxygen
OH2  OH   -0.950015.998  1H  0.100 ;hydroxyl oxygen
O2   obts  -1.1688  15.998  0;bridging oxygen with
tetrahedral substitution
O1   obss  -1.2996  15.998  0 ;bridging oxygen with
double substitution
OH1  ohs   -1.0808   15.998  1  H  0.100   ;hydroxyl hydrogen with
substitution
Si   st2.100028.086  0 ;tetrahedral silicon
Al   ao1.575026.982  0 ;octahedral aluminium
Mg  mgo1.360024.305  0 ; octahedral magnisium
Na   Na1.22.999  0 ;sodium ion

forcefield.doc
clayff.ff force field

forcefield.itp
#define _ff_clayff


[ defaults ]
 ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
 1   3   yes 0.5 0.5

#include "ffnonbonded.itp"
#include "ffbonded.itp"

pdb

Al0.6494.3333.377
Al3.248.8053.377
Al3.2032.8513.362
Al0.6397.3243.362
Si4.9623.0160.65
Si2.3987.4880.65
Si2.4421.470.653
Si-0.1225.9420.653
O1-0.3343.0982.268
O12.2587.572.268
O10.0415.8392.271
O12.6051.3672.271
O30.0144.4720
O3-1.8854.2597.154
O35.1694.4720
O33.274.2597.154
O32.57800
O30.678-0.2147.154
O32.6058.9450
O30.7068.7317.154
O31.0342.0560.177
O33.6266.5290.177
O31.0526.8480.023
O33.6162.3760.023
OH1-0.3228.6062.304
OH12.2424.1332.304
OH23.831.364.329
OH21.2665.8324.329
OH2-0.9624.1364.35
OH21.6298.6084.35
OH2-0.9617.5354.36
OH21.6023.0634.36
O22.63310.3122.271
OH23.85810.3054.329
OH24.8348.6062.304
OH24.1947.5354.36
O34.8213.0982.268
OH34.1934.1364.35
O36.192.0560.177
O3-1.5296.5290.177


It's to long, Sorry about it, but I really need to find out where is my
problem. I put n2t file in directory not in my forcefield subdirectory. Do
I need to create any other file for clayff forcefield?

Thank you in advece,
Golnaz
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[gmx-users] RDF

[Vidya R]

Hi,

I want to calculate RDF of my organic molecule with a solvent.

What should be the duration of my simulation?

Is 100 ps enough?


Thanks,
Vidya.R
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Re: [gmx-users] TIP4P/ice pdb file

[G R]

Dear Chris,

Yes, tip4p.gro worked well.

Thank you

On Wed, Jul 5, 2017 at 10:55 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users@maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>1. TIP4P/ice pdb file (G R)
>2. Re: simulation at different temperature (Alex)
>3. Re: simulation at different temperature (Alex)
>4. Re: TIP4P/ice pdb file (Christopher Neale)
>5. Re: TIP4P/ice pdb file (Christopher Neale)
>
>
> --
>
> Message: 1
> Date: Wed, 5 Jul 2017 21:57:26 +0300
> From: G R <golnaz.c...@gmail.com>
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] TIP4P/ice pdb file
> Message-ID:
> 

[gmx-users] TIP4P/ice pdb file

[G R]

Dear All,

I would like to simulate water using TIP4P/ice potential. My question is
that how can I generate .gro file for this simulation?
I will use TIP4P/ice topology that is available in SklogWiki, but I cannot
understand how can I generate .gro file for this topology. Can I easily use
TIP4P.gro that is available in share/top? If yes, how can I modify
TIP4P.gro file to use with TIP4P/ice potential?

Best regards,
Golnaz
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[gmx-users] TOPOLOGY USING OPLS FORCEFIELD

[Vidya R]

Hi gromacs users,

After getting the output from topolbuild, how to construct topology file
using opls forcefield?

Can anyone send useful links for the same?

Thanks,
Vidya.R
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[gmx-users] compiling ambconv

[Vidya R]

Hi gromacs users,

How to compile ambconv extracted from ambconv.tgz?


Thanks,
Vidya R
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[gmx-users] GETTING GOOD PERFORMANCE FROM MDRUN

[Vidya R]

Hi,

How to get good (and fast) performance from mdrun through available 8
logical CPU cores?

When I gave,

gmx mdrun -ntmpi 2 -ntomp 4 -v -deffnm eq

It seems to be slow, much slower than

gmx mdrun -v -deffnm eq.

Can anyone help?

Thanks,
Vidya R
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[gmx-users] clayff forcefield

[G R]

Dear usres,

I try to write clayff forcefield, and I want to simulate Kaolinite. I have
some questions about it.
1) should I write clayff forcefield separately or modify one of the
forcefields in share/top?
2) The directory for clayff forcefield should be included ffbonded.itp,
ffnonbonded.itp, atomname2type.n2t, forcefield.itp,
forcefield.doc,atomtype.atp? if it is needed any other file please let me
know?
3) In .n2t file, the first column should be written corresponding .gro
file?
4) For Kaolinite I only have two type of Oxygen, ob (bridging oxygen) and
oh (oxygen in hydroxyl group). Am I right?

Any help will be appreciated,
Golnaz
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[gmx-users] Simulation of pure water

[G R]

Dear all,

I want to calculate the relaxation of pure water cell at room temperature
and at freezing point, monitoring its equilibration in volume and in
potential energy. I have 3 question: 1) Can I use packmol for my initial
configuration? if there is any other option,please tell me. 2) Can I use
easily pdb2gmx to generate the topology file? 3) Which Forcefield is better
for this calculation?

I'v already read some tutorial, but if you have any suggestion it woulb be
appreciated.

Thank you in advance
 GR
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[gmx-users] Simulation of pure water

[G R]

Dear all,

I want to calculate the relaxation of pure water cell at room temperature
and at freezing point, monitoring its equilibration in volume and in
potential energy. I have 3 question: 1) Can I use packmol for my initial
configuration? if there is any other option,please tell me. 2) Can I use
easily pdb2gmx to generate the topology file? 3) Which Forcefield is better
for this calculation?

I'v already read some tutorial, but if you have any suggestion it woulb be
appreciated.

Thank you in advanc
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[gmx-users] how to fix pme number

[Vidya R]

Hi gromacs users,

In this command,

gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm eql2

how to determine the value of pme..

I want to include -npme...

Please help


Thanks,
Vidya.R
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[gmx-users] gmx tune_pme

[Vidya R]

Hi gromacs users,

When i tried using,

gmx tune_pme -np 8 -s eql2.tpr -launch

Got this error..

How to fix it?

[compute-0-3.local:28193] [[20294,1],0] ORTE_ERROR_LOG: A message is
attempting to be sent to a process whose contact information is unknown in
file rml_oob_send.c at line 105
[compute-0-3.local:28193] [[20294,1],0] could not get route to
[[INVALID],INVALID]

Thanks,
Vidya.R
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[gmx-users] what is the difference between gmx mdrun and gmx tune_pme

[Vidya R]

Hi gromacs users,

What is the difference between gmx mdrun and gmx tune_pme? Which is better
to use in a cluster (especially when we submit our jobs through qsub
command?)




Also, what is the purpose of -np option in gmx tune_pme? Can someone
elucidate?


Thanks,
Viday.R
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[gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

[Vidya R]

My log file is provided in the link below

Can you please look into it and let me know why the error arises?

I am feeding my commands in SGE cluster.   When I run it in my login node,
gmx mdrun -v -deffnm eql runs well


But, through qsub command, (with 8 processors) It says,

mpirun noticed that process rank 7 with PID 19160 on node
compute-0-28.local exited on signal 11 (Segmentation fault).

Please help me.

I am unable to figure out, as to whether the problem is with the version of
gromacs or the method of compiling.


https://drive.google.com/file/d/0BxGqxeGwTDLbQW9OZDFuM1doUlU/view?usp=sharing
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Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

[Vidya R]

https://drive.google.com/file/d/0BxGqxeGwTDLbLWJ5SExDblVhRFU
/view?usp=sharing=59be86ad

On Sun, Sep 17, 2017 at 6:35 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 9/17/17 1:22 AM, Vidya R wrote:
>
>> My log file is provided in the link below
>>
>> Can you please look into it and let me know why the error arises?
>>
>> I am feeding my commands in SGE cluster.   When I run it in my login node,
>> gmx mdrun -v -deffnm eql runs well
>>
>>
>> But, through qsub command, (with 8 processors) It says,
>>
>> mpirun noticed that process rank 7 with PID 19160 on node
>> compute-0-28.local exited on signal 11 (Segmentation fault).
>>
>> Please help me.
>>
>> I am unable to figure out, as to whether the problem is with the version
>> of
>> gromacs or the method of compiling.
>>
>>
>> https://drive.google.com/file/d/0BxGqxeGwTDLbQW9OZDFuM1doUlU
>> /view?usp=sharing
>>
>>
> I am unable to view the file, as it says I do not have permission.  Please
> change the access restrictions on it.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
> --
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Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

[Vidya R]

Thank you for your reply.

When I try to run my job in a single processor through qsub command, (by
feeding the gromacs mdrun command in script file), it says SEGMENTATION
FAULT, CORE DUMPED...


But, when I run my job in login node (which we are not supposed to do), it
works very well...


Can you comment on this?


Thanks,
Vidya.R

On Mon, Sep 18, 2017 at 2:50 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> You're running a thread-MPI version of GROMACS, which is probably not what
> you want to do if you're running mpirun. It should work even so, but
> whatever quirks exist with SGE are unfortunately between you, its docs and
> your cluster's docs and admins :-(
>
> Mark
>
> On Sun, Sep 17, 2017 at 7:23 AM Vidya R <vidyadevi2...@gmail.com> wrote:
>
> > My log file is provided in the link below
> >
> > Can you please look into it and let me know why the error arises?
> >
> > I am feeding my commands in SGE cluster.   When I run it in my login
> node,
> > gmx mdrun -v -deffnm eql runs well
> >
> >
> > But, through qsub command, (with 8 processors) It says,
> >
> > mpirun noticed that process rank 7 with PID 19160 on node
> > compute-0-28.local exited on signal 11 (Segmentation fault).
> >
> > Please help me.
> >
> > I am unable to figure out, as to whether the problem is with the version
> of
> > gromacs or the method of compiling.
> >
> >
> >
> > https://drive.google.com/file/d/0BxGqxeGwTDLbQW9OZDFuM1doUlU/
> view?usp=sharing
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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[gmx-users] selecting atoms in index file

[G R]

Dear All,

I want to create an index file and select some especial atoms in a surface.
My problem is that I have only one residue for the whole surface. How can I
select the atoms on the surface as a different groups in my index file?

Thank you in advance,
Golnaz
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Re: [gmx-users] selecting atoms in index file

[G R]

On Thu, Sep 7, 2017 at 12:35 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users@maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
> gromacs.org_gmx-users-requ...@maillist.sys.kth.se
>
> You can reach the person managing the list at
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>1. Re: selecting atoms in index file (Hermann, Johannes)
>2. Re: DPOSRES not working (Hermann, Johannes)
>3. Re: DPOSRES not working (Sergio Manzetti)
>4. Re: DPOSRES not working (Hermann, Johannes)
>5. Re: DPOSRES not working (Sergio Manzetti)
>
>
> --
>
> Message: 1
> Date: Thu, 7 Sep 2017 11:16:08 +0200
> From: "Hermann, Johannes" <j.herm...@lrz.tu-muenchen.de>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] selecting atoms in index file
> Message-ID: <c1fd2b6b-91f9-5ec7-d39d-4b666599a...@lrz.tum.de>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Dear Golnaz,
>
> do you know the number (index) of the respective atoms? E.g. open the
> .gro file in vmd and look for the atoms?
>
> If there are not too many atoms, you can manually edit your index file.
> E.g. create a default index file (gmx make_ndx) and add the subset of
> indexes with a new selection definition:
>
> ---
>
> [ MySelection]
>
> 23 57 75
>
> ---
>
> All the best
>
> Johannes
>
> Hi Johanne,
>
> Thank you for your reply. just one more question: when I edit atoms in my
> index file, should I delete these atoms from surfaces groups. let me
> explain better. Now I have 2 groups in my index file Sol and
> Kaoli(surface). I should select some atoms from the Kaoli. So first I
> define the atoms that I want to select in a seperate group, then I should
> erase these atoms from kaoli parts. Am I right?  because I want to freeze
> the surface without these atoms.
>
> On 07.09.2017 11:02, G R wrote:
> > Dear All,
> >
> > I want to create an index file and select some especial atoms in a
> surface.
> > My problem is that I have only one residue for the whole surface. How
> can I
> > select the atoms on the surface as a different groups in my index file?
> >
> > Thank you in advance,
> > Golnaz
>
> --
> __
> *Technische Universit?t M?nchen*
> *Johannes Hermann, M.Sc.*
> Lehrstuhl f?r Bioverfahrenstechnik
> Boltzmannstr. 15
> D-85748 Garching
> Tel: +49 8928915730
> Fax: +49 8928915714
>
> Email: j.herm...@lrz.tum.de
> http://www.biovt.mw.tum.de/
>
>
>
> --
>
> Message: 2
> Date: Thu, 7 Sep 2017 11:18:29 +0200
> From: "Hermann, Johannes" <j.herm...@lrz.tu-muenchen.de>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] DPOSRES not working
> Message-ID: <8c01673e-77d8-fa16-c5ad-ec0269a47...@lrz.tum.de>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Dear Sergio,
>
> how did you define the position restrain in your topology? Check your
> topology and position restrain file.
>
> All the best
>
> Johannes
>
>
> On 07.09.2017 11:07, Sergio Manzetti wrote:
> > Hello, I am running 5 simulations with the given mdp:
> >
> > title = DNA in water stabilization
> > cpp = /lib/cpp
> > include = -I../top
> > define = -DPOSRES
> > integrator = md
> > dt = 0.002
> > nsteps = 1000
> > nstxout = 5000
> > nstvout = 5000
> > nstlog = 5000
> > nstenergy = 300
> > nstxout-compressed = 300
> > compressed-x-grps = PRB SOL NA CL DNA
> > energygrps = PRB SOL NA CL DNA
> > nstlist = 10
> > ns-type = grid
> > rlist = 0.8
> > coulombtype = PME
> > rcoulomb = 0.8
> > rvdw = 0.8
> > tcoupl = V-Rescale
> > tc-grps = System
> > tau-t = 0.1
> > ref-t = 310
> > Pcoupl = No
> > tau-p = 1.0
> > compressibility = 4.5e-5
> > ref-p = 1.0
> > gen-vel = yes
> > gen-temp = 310
> > gen-seed = 17527
> > constraints = all-bonds
> >
> >
> > and still, the DNA splits into two
> >
> > Any ideas what could be wrong?
> >
> > Thanks
> &

[gmx-users] gromacs error

[Vidya R]

Hi,


When I give these two commands

gmx grompp -f mdp/min.mdp -o min -pp min -po min
gmx mdrun -deffnm min

I get this error.

What to do?



Reading file min.tpr, VERSION 5.0.2 (single precision)
tMPI error: tMPI Initialization error (in valid comm)

Thanks,
Vidya.R
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[gmx-users] error sharing libraries...gromacs error

[Vidya R]

Hi,

I give these commands

PATH=$PATH:"/usr/local/gromacs/bin/"
export GMXLIB=/usr/local/gromacs/share/gromacs/top
export LD_LIBRARY_PATH=/usr/lib
export MPIRUN="/usr/mpi/pgi/openmpi-1.2.8/bin/mpirun"
export
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/ansys_inc/v140/CFX/tools/icemcfd-12.0-post-3/lib/linux-amd64


before these

gmx grompp -f mdp/min.mdp -o min -pp min -po min
g_tune_pme -np 4 -s min.tpr -launch



But, I am getting this error

/usr/mpi/pgi/openmpi-1.2.8/bin/mpirun: error while loading shared
libraries: libpgc.so: cannot open shared object file: No such file or
directory


But libpgc.so is in
/usr/ansys_inc/v140/CFX/tools/icemcfd-12.0-post-3/lib/linux-amd64

What to do?

Can someone help me with the commands?

Thanks,
Vidya.R
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Re: [gmx-users] error sharing libraries...gromacs error

[Vidya R]

Hi,

I now use

export MPIRUN="/usr/mpi/gcc/openmpi-1.2.8/bin"

But, how to fix that error?

Thanks,
Vidya.R

On Tue, Sep 12, 2017 at 5:42 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> If you're trying to use the PGI compilers, then please don't because the
> C++ performance is very poor. We recommend latest gcc or intel.
>
> Otherwise, configure GROMACS so that it uses the wrapper compilers when
> buildling, e.g. cmake -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpic++
> etc. Organizing this stuff is their job.
>
> Mark
>
> On Tue, Sep 12, 2017 at 1:46 PM Vidya R <vidyadevi2...@gmail.com> wrote:
>
> > Hi,
> >
> > I give these commands
> >
> > PATH=$PATH:"/usr/local/gromacs/bin/"
> > export GMXLIB=/usr/local/gromacs/share/gromacs/top
> > export LD_LIBRARY_PATH=/usr/lib
> > export MPIRUN="/usr/mpi/pgi/openmpi-1.2.8/bin/mpirun"
> > export
> >
> > LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/ansys_inc/v140/CFX/
> tools/icemcfd-12.0-post-3/lib/linux-amd64
> >
> >
> > before these
> >
> > gmx grompp -f mdp/min.mdp -o min -pp min -po min
> > g_tune_pme -np 4 -s min.tpr -launch
> >
> >
> >
> > But, I am getting this error
> >
> > /usr/mpi/pgi/openmpi-1.2.8/bin/mpirun: error while loading shared
> > libraries: libpgc.so: cannot open shared object file: No such file or
> > directory
> >
> >
> > But libpgc.so is in
> > /usr/ansys_inc/v140/CFX/tools/icemcfd-12.0-post-3/lib/linux-amd64
> >
> > What to do?
> >
> > Can someone help me with the commands?
> >
> > Thanks,
> > Vidya.R
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] gromacs error

[Vidya R]

Hi,

I fixed that error.

However,I now encounter a new one...

GROMACS:gmx grompp, VERSION 5.0.2

GROMACS is written by:
Emile Apol Rossen Apostolov   Herman J.C. Berendsen Par
Bjelkmar
Aldert van Buuren  Rudi van DrunenAnton Feenstra Sebastian Fritsch
Gerrit GroenhofChristoph Junghans Peter Kasson   Carsten Kutzner
Per LarssonJustin A. Lemkul   Magnus LundborgPieter Meulenhoff
Erik Marklund  Teemu Murtola  Szilard Pall   Sander Pronk
Roland Schulz  Alexey ShvetsovMichael Shirts Alfons Sijbers
Peter Tieleman Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2014, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx grompp, VERSION 5.0.2
Executable:   /usr/local/gromacs/bin/gmx
Library dir:  /usr/local/gromacs/share/gromacs/top
Command line:
  gmx grompp -f mdp/min.mdp -o min -pp min -po min

Setting the LD random seed to 1842076191
Generated 349030 of the 349030 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 349030 of the 349030 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'LIG'
Excluding 2 bonded neighbours molecule type 'SOL'
Removing all charge groups because cutoff-scheme=Verlet
Number of degrees of freedom in T-Coupling group rest is 11837.00
Estimate for the relative computational load of the PME mesh part: 0.17

gcq#309: "Nobody Never Learnt No-Nothing from No History" (Gogol Bordello)

GROMACS:gmx mdrun, VERSION 5.0.2

GROMACS is written by:
Emile Apol Rossen Apostolov   Herman J.C. Berendsen Par
Bjelkmar
Aldert van Buuren  Rudi van DrunenAnton Feenstra Sebastian Fritsch
Gerrit GroenhofChristoph Junghans Peter Kasson   Carsten Kutzner
Per LarssonJustin A. Lemkul   Magnus LundborgPieter Meulenhoff
Erik Marklund  Teemu Murtola  Szilard Pall   Sander Pronk
Roland Schulz  Alexey ShvetsovMichael Shirts Alfons Sijbers
Peter Tieleman Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2014, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx mdrun, VERSION 5.0.2
Executable:   /usr/local/gromacs/bin/gmx
Library dir:  /usr/local/gromacs/share/gromacs/top
Command line:
  gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm min

Reading file min.tpr, VERSION 5.0.2 (single precision)
Using 1 MPI thread
Using 8 OpenMP threads
mpirun noticed that job rank 0 with PID 18038 on node compute-0-20.local
exited on signal 11 (Segmentation fault).


What is segmentation fault?

What am I supposed to do?

Please tell me.

Thanks,
Vidya.R


On Mon, Sep 11, 2017 at 7:27 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Yeah I've never seen that, so I assume it's something weird related to how
> GROMACS was originally compiled vs how the system has been updated since.
> Since a rebuild is the way to investigate that, definitely update to at
> least the latest 5.0.x while you do it.
>
> Mark
>
> On Mon, Sep 11, 2017 at 3:36 PM Wes Barnett <w.barn...@columbia.edu>
> wrote:
>
> > On Mon, Sep 11, 2017 at 8:44 AM, Vidya R <vidyadevi2...@gmail.com>
> wrote:
> >
> > > Hi,
> > >
> > >
> > > When I give these two commands
> > >
> > > gmx grompp -f mdp/min.mdp -o min -pp min -po min
> > > gmx mdrun -deffnm min
> > >
> > > I get this error.
> > >
> > > What to do?
> > >
> > >
> > >
> > > Reading file min.tpr, VERSION 5.0.2 (single precision)
> > > tMPI error: tMPI Initialization error (in valid comm)
> > >
> > > Thanks,
> > > Vidya.R
> > >
> >
> > I can't speak to that exact error, but there have been several bug fix
> > releases to the 5.0.x series since 5.0.2, so an upgrade may be in order.
&g

[gmx-users] DSSP

[Vidya R]

Hi gromacs users,

I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.)

I want to download and install dssp tool.

How to proceed?


Thanks,
Vidya.R
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Re: [gmx-users] DSSP

[Vidya R]

I got the error

dssp cmd='/usr/local/bin -i ddpEbgmY -o ddtFRo32 > /dev/null 2> /dev/null'
Reading frame   0 time0.000
Back Off! I just backed up ddpEbgmY to ./#ddpEbgmY.1#

---
Program gmx do_dssp, VERSION 5.1.4
Source code file:
/cygdrive/d/software/GROMACS/gromacs-5.1.4/src/gromacs/gmxana/

gmx_do_dssp.c, line: 663

Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver
option  .

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


On Tue, Dec 5, 2017 at 6:36 PM, João Henriques <joao.m.a.henriq...@gmail.com
> wrote:

> Hi!
>
> This is not so much for you as it is for the other users and developers. I
> think I found a problem with the DSSP code when compiling using the latest
> boost version (1.65.1). "tr1/tuple.hpp" cannot be found within the
> "include" directory of this new boost, and the compilation fails. The error
> is reproducible if you instead use homebrew to install DSSP.
>
> I've emailed Maarten at "m.hekkel...@cmbi.ru.nl" but I'm not sure this
> email is active anymore. Hopefully it is, otherwise please let me know.
>
> Best regards,
> J
>
> On Tue, Dec 5, 2017 at 6:38 AM, Vidya R <vidyadevi2...@gmail.com> wrote:
>
> > Hi gromacs users,
> >
> > I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.)
> >
> > I want to download and install dssp tool.
> >
> > How to proceed?
> >
> >
> > Thanks,
> > Vidya.R
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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