RE: [gmx-users] problem with the size of freeze groups
Hi, I don't know exactly what you have done, so currently I can say more than I have done already. Could you please file a bugzilla at bugzilla.gromacs.org and attach all the files required to run grompp? Thanks, Berk Date: Tue, 2 Mar 2010 21:11:06 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, Thanks for your previous responses, Can you please let me know if you have any solution for the size of freezing groups? I am still not able to do if i have larger freezing groups. Thanks again for your kind help. srinivas. On Fri, Feb 26, 2010 at 5:37 PM, jampani srinivas jampa...@gmail.com wrote: Dear Berk, I have checked my inputs and tcl scripts that i have used for the selection, i could see that my selection doesn't have any problem. I submitted it again still i am getting the same log file with nrdf 0 for non-freezing group. Please let me know if you want see any of my input files, and help me if you have solution for this problem. Thanks and RegardsSrinivas. On Fri, Feb 26, 2010 at 12:39 PM, jampani srinivas jampa...@gmail.com wrote: Dear Berk, I am using VERSION 4.0.5. As you said if there is no problem i should get it correctly, i don't know where it is going wrong. I have written a small script in tcl to use in vmd to get my selections. i will check the script and the selection again. I will let you know my results again. Thanks for your valuable time and kind help.Srinivas. On Fri, Feb 26, 2010 at 12:29 PM, Berk Hess g...@hotmail.com wrote: Hi, Which version of Gromacs are you using? I can't see any issues in the 4.0 code, but some older version might have problems. Berk Date: Fri, 26 Feb 2010 12:05:56 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, They are same, freeze and Tmp2 are exactly the same groups. I just put them like that for my convenience, just to avoid confusion in my second email i made it uniform. ThanksSrinivas. On Fri, Feb 26, 2010 at 11:59 AM, Berk Hess g...@hotmail.com wrote: That is what I suspected, by I don't know why this is. Are you really sure you made a temperature coupling group that is exactly the freeze group? This first mdp file you mailed had a different group names for the freeze group and the tcoupl groups. Berk Date: Fri, 26 Feb 2010 11:53:49 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, It looks to me some thing is wrong when i change the radius from 35 to 25, herewith i am giving grpopts for both systems + grpopts: (system with 35 A) nrdf: 33141.4 0 ref_t: 300 0 tau_t: 0.1 0.1+ grpopts: (system with 25A) nrdf: 0 0 ref_t: 300 0 tau_t: 0.1 0.1 I think some thing is going wrong when the size of freezing group is increased. I don't know whether my understand is correct or not. Thanks Srinivas. On Fri, Feb 26, 2010 at 11:01 AM, Berk Hess g...@hotmail.com wrote: Ah, but that does not correspond to the mdp options tou mailed. Here there is only one group with 0 degrees of freedom and reference temperature 0. Berk Date: Fri, 26 Feb 2010 10:50:13 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org HI Thanks, My log file shows me nrdf: 0 ### grpopts: nrdf: 0 ref_t:0 tau_t: 0 ### ThanksSrinivas. On Fri, Feb 26, 2010 at 10:25 AM, Berk Hess g...@hotmail.com wrote: Hi, Then I have no clue what might be wrong. Have you check nrdf in the log file? Berk Date: Fri, 26 Feb 2010 09:54:22 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, Thanks for your response, As you mentioned i have separated t-coupling group for frozen and non-frozen groups, still the result is same.Herewith i am giving my md.mdp file, Can you suggest me if i am missing any options in my md.mdp file? Thanks againSrinivas. md.mdp file +++title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 150 ; total 3.0 ns. nstcomm = 1 nstxout = 1000 ; collect data every 2.0 ps nstvout = 1000 ; collect velocity every 2.0 ps nstfout = 0 nstlog = 0 nstenergy = 1000 ; collect energy every 2.0 ps nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb
Re: [gmx-users] gromacs memory usage
Hi Roland, It says gromacs/4.0.5/bin/mdrun_mpi: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), for GNU/Linux 2.6.9, not stripped On Tue, Mar 2, 2010 at 10:34 PM, Roland Schulz rol...@utk.edu wrote: Amit, try the full line (with the file) Roland On Wed, Mar 3, 2010 at 1:22 AM, Amit Choubey kgp.a...@gmail.com wrote: Hi Roland I tried 'which mdrun' but it only gives the path name of installation. Is there any other way to know if the installation is 64 bit ot not? Thank you, Amit On Tue, Mar 2, 2010 at 10:03 PM, Roland Schulz rol...@utk.edu wrote: Hi, do: file `which mdrun` and it should give: /usr/bin/mdrun: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.15, stripped If it is not 64 you need to compile with 64 and have a 64bit kernel. Since you asked before about 2GB large files this might indeed be your problem. Roland On Wed, Mar 3, 2010 at 12:48 AM, Amit Choubey kgp.a...@gmail.comwrote: Hi Tsjerk, I tried to do a test run based on the presentation. But there was a memory related error (I had given a leverage of more than 2 GB). I did not understand the 64 bit issue, could you let me know wheres the documentation? I need to look into that. Thank you, amit On Tue, Mar 2, 2010 at 9:14 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Amit, I think the presentation gives right what you want: a rough estimate. Now as Berk pointed out, to allocate more than 2GB of memory, you need to compile in 64bit. Then, if you want to have a real feel for the memory usage, there's no other way than trying. But fortunately, the memory requirements of a (very) long simulation are equal to that of a very short one, so it doesn't need to cost much time. Cheers, Tsjerk On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey kgp.a...@gmail.com wrote: Hi Mark, Yes thats one way to go about it. But it would have been great if i could get a rough estimation. Thank you. amit On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 3/03/2010 12:53 PM, Amit Choubey wrote: Hi Mark, I quoted the memory usage requirements from a presentation by Berk Hess, Following is the link to it http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf l. In that presentation on pg 27,28 Berk does talk about memory usage but then I am not sure if he referred to any other specific thing. My system only contains SPC water. I want Berendsen T coupling and Coulomb interaction with Reaction Field. I just want a rough estimate of how big of a system of water can be simulated on our super computers. Try increasingly large systems until it runs out of memory. There's your answer. Mark On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: - Original Message - From: Amit Choubey kgp.a...@gmail.com mailto: kgp.a...@gmail.com Date: Saturday, February 27, 2010 10:17 Subject: Re: [gmx-users] gromacs memory usage To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Hi Mark, We have few nodes with 64 GB memory and many other with 16 GB of memory. I am attempting a simulation of around 100 M atoms. Well, try some smaller systems and work upwards to see if you have a limit in practice. 50K atoms can be run in less than 32GB over 64 processors. You didn't say whether your simulation system can run on 1 processor... if it does, then you can be sure the problem really is related to parallelism. I did find some document which says one need (50bytes)*NATOMS on master node, also one needs (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute nodes. Is this true? In general, no. It will vary with the simulation algorithm you're using. Quoting such without attributing the source or describing the context is next to useless. You also dropped a parenthesis. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www
[gmx-users] parallel simulations
Hi all
My apologies for the lack of detail in my previous e-mail. I am trying
to run gromacs-4.0.7 for a system that I am studying. I have ran several
simulations on serial on my own computer that have to date worked fine.
I am now however trying to run the simulations on our local cluster in
parallel using mpich-1.2.7 and experiencing some difficulty. Please note
that the version of gromacs mentioned above is installed in parallel.
Right when I run a short simulation of 500 steps in one two or three nodes the
simulations
runs fine (takes about 10 seconds) and all the data is written to the
log file. However when I increase the nodes to 4 there is no stepwise
info written and the simulation does not progress. For clarity I have
attached the log file that iam getting for the 4 node simulation. I realise that
this maybe a cluster problem, but if anyone has experienced similar
issues I would be grateful of some feedback.
Here is the script I use:
#!/bin/bash
#PBS -N hex
#PBS -r n
#PBS -q longterm
#PBS -l walltime=00:30:00
#PBS -l nodes=4
cd $PBS_O_WORKDIR
export P4_GLOBMEMSIZE=1
/usr/local/bin/mpiexec mdrun -s
Also here is my path:
# Gromacs
export GMXLIB=/k/gavin/gromacs-4.0.7-parallel/share/gromacs/top
export PATH=$PATH:/k/gavin/gromacs-4.0.7-parallel/bin
Cheers
Gavin
Log file opened on Wed Mar 3 14:46:51 2010
Host: kari57 pid: 32586 nodeid: 0 nnodes: 4
The Gromacs distribution was built Wed Jan 20 10:02:46 GMT 2010 by
ga...@kari (Linux 2.6.17asc64 x86_64)
:-) G R O M A C S (-:
GROningen MAchine for Chemical Simulation
:-) VERSION 4.0.7 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun (-:
PLEASE READ AND CITE THE FOLLOWING REFERENCE
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
--- Thank You ---
parameters of the run:
integrator = md
nsteps = 500
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode= Linear
nstlog = 25
nstxout = 25
nstvout = 25
nstfout = 25
nstenergy= 25
nstxtcout= 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 35
nky = 35
nkz = 35
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = Nose-Hoover
epc = Parrinello-Rahman
epctype = Isotropic
tau_p= 1
ref_p (3x3):
ref_p[0]={ 1.01325e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 1.01325e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 1.01325e+00}
compress (3x3):
compress[0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 4.5e-05}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]=
Re: [gmx-users] gromacs memory usage
Hi, ok then it is compiled in 64bit. You didn't say how many cores each node has and on how many nodes you want to run. Roland On Wed, Mar 3, 2010 at 4:32 AM, Amit Choubey kgp.a...@gmail.com wrote: Hi Roland, It says gromacs/4.0.5/bin/mdrun_mpi: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), for GNU/Linux 2.6.9, not stripped On Tue, Mar 2, 2010 at 10:34 PM, Roland Schulz rol...@utk.edu wrote: Amit, try the full line (with the file) Roland On Wed, Mar 3, 2010 at 1:22 AM, Amit Choubey kgp.a...@gmail.com wrote: Hi Roland I tried 'which mdrun' but it only gives the path name of installation. Is there any other way to know if the installation is 64 bit ot not? Thank you, Amit On Tue, Mar 2, 2010 at 10:03 PM, Roland Schulz rol...@utk.edu wrote: Hi, do: file `which mdrun` and it should give: /usr/bin/mdrun: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.15, stripped If it is not 64 you need to compile with 64 and have a 64bit kernel. Since you asked before about 2GB large files this might indeed be your problem. Roland On Wed, Mar 3, 2010 at 12:48 AM, Amit Choubey kgp.a...@gmail.comwrote: Hi Tsjerk, I tried to do a test run based on the presentation. But there was a memory related error (I had given a leverage of more than 2 GB). I did not understand the 64 bit issue, could you let me know wheres the documentation? I need to look into that. Thank you, amit On Tue, Mar 2, 2010 at 9:14 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Amit, I think the presentation gives right what you want: a rough estimate. Now as Berk pointed out, to allocate more than 2GB of memory, you need to compile in 64bit. Then, if you want to have a real feel for the memory usage, there's no other way than trying. But fortunately, the memory requirements of a (very) long simulation are equal to that of a very short one, so it doesn't need to cost much time. Cheers, Tsjerk On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey kgp.a...@gmail.com wrote: Hi Mark, Yes thats one way to go about it. But it would have been great if i could get a rough estimation. Thank you. amit On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 3/03/2010 12:53 PM, Amit Choubey wrote: Hi Mark, I quoted the memory usage requirements from a presentation by Berk Hess, Following is the link to it http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf l. In that presentation on pg 27,28 Berk does talk about memory usage but then I am not sure if he referred to any other specific thing. My system only contains SPC water. I want Berendsen T coupling and Coulomb interaction with Reaction Field. I just want a rough estimate of how big of a system of water can be simulated on our super computers. Try increasingly large systems until it runs out of memory. There's your answer. Mark On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: - Original Message - From: Amit Choubey kgp.a...@gmail.com mailto: kgp.a...@gmail.com Date: Saturday, February 27, 2010 10:17 Subject: Re: [gmx-users] gromacs memory usage To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Hi Mark, We have few nodes with 64 GB memory and many other with 16 GB of memory. I am attempting a simulation of around 100 M atoms. Well, try some smaller systems and work upwards to see if you have a limit in practice. 50K atoms can be run in less than 32GB over 64 processors. You didn't say whether your simulation system can run on 1 processor... if it does, then you can be sure the problem really is related to parallelism. I did find some document which says one need (50bytes)*NATOMS on master node, also one needs (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute nodes. Is this true? In general, no. It will vary with the simulation algorithm you're using. Quoting such without attributing the source or describing the context is next to useless. You also dropped a parenthesis. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list
[gmx-users] GPU GROMACS
Is anyone working on a build GROMACS with CUDA other than the OpenMM project? I would like to build this with explicit solvents and as I understand it, OpenMM is implicit. -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] parallel simulations
Hi all
My apologies for the lack of detail in my previous e-mail. I am trying
to run gromacs-4.0.7 for a system that I am studying. I have ran several
simulations on serial on my own computer that have to date worked fine.
I am now however trying to run the simulations on our local cluster in
parallel using mpich-1.2.7 and experiencing some difficulty. Please note
that the version of gromacs mentioned above is installed in parallel.
Right when I run a short simulation of 500 steps in one two or three
nodes the simulations
runs fine (takes about 10 seconds) and all the data is written to the
log file. However when I increase the nodes to 4 there is no stepwise
info written and the simulation does not progress. For clarity I have
attached the log file that iam getting for the 4 node simulation. I
realise that
this maybe a cluster problem, but if anyone has experienced similar
issues I would be grateful of some feedback.
Here is the script I use:
#!/bin/bash
#PBS -N hex
#PBS -r n
#PBS -q longterm
#PBS -l walltime=00:30:00
#PBS -l nodes=4
cd $PBS_O_WORKDIR
export P4_GLOBMEMSIZE=1
/usr/local/bin/mpiexec mdrun -s
Also here is my path:
# Gromacs
export GMXLIB=/k/gavin/gromacs-4.0.7-parallel/share/gromacs/top
export PATH=$PATH:/k/gavin/gromacs-4.0.7-parallel/bin
Cheers
Gavin
Log file opened on Wed Mar 3 14:46:51 2010
Host: kari57 pid: 32586 nodeid: 0 nnodes: 4
The Gromacs distribution was built Wed Jan 20 10:02:46 GMT 2010 by
ga...@kari (Linux 2.6.17asc64 x86_64)
:-) G R O M A C S (-:
GROningen MAchine for Chemical Simulation
:-) VERSION 4.0.7 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun (-:
PLEASE READ AND CITE THE FOLLOWING REFERENCE
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
--- Thank You ---
parameters of the run:
integrator = md
nsteps = 500
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode= Linear
nstlog = 25
nstxout = 25
nstvout = 25
nstfout = 25
nstenergy= 25
nstxtcout= 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 35
nky = 35
nkz = 35
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = Nose-Hoover
epc = Parrinello-Rahman
epctype = Isotropic
tau_p= 1
ref_p (3x3):
ref_p[0]={ 1.01325e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 1.01325e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 1.01325e+00}
compress (3x3):
compress[0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 4.5e-05}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]=
[gmx-users] NVT simulation and mdp file
Dear Gromacs Users, I have encountered the following issues while I was running my MD simulation. Can anybody comment on what the meaning of these notes are. Is there anything I could do to avoid them. NOTE 2 [file PAP.top, line unknown]: The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. My SOLVENT IS TOLUENE --- the PRODRG gave me a topology file with only one group charge only. NOTE 1 [file nvt.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. NOTE 3 [file aminoacids.dat, line 1]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing In addition to the above notes I have also some questions about the NVT and NPT simulation. 1)I am using toluene as a solvent to simulate my polymer, do I need to use the compressibility of toluene which is 9.2e-5 or the default value 4.5e-5 1/bar. 2)What about the dielectric constant (the dielectric constant for toluene is 2-2.4), but the default value is 80 ( I assume this is for water- am I right). 3)Is always rvdw = 1.4 nm for GROMOS96. As a result I have to increase my box size of the solute at the beginning to a min of 2*1.4 =2.8 ( min image convection). Is this the right way to do! 4)I run an NVT simulation to equilibrate my system for 100 ps. When I checked my simulation at the end (successfully completed) I noticed that the shape of my simulation box looks CIRCULAR! some how the rectangular shape looks distorted. What does this tell! Do you guys think something is wrong in my simulation. 5)I included the polar and aromatic hydrogens in my simulation ( ffG43a1.itp GROMOS96.1 in PRODRG). Does these hydrogen influence my result as the force field is a united atom force field. Or How can I get rid of them if I want. With or without the aromatic hydrogen gave good results ( besides lower computational cost). Does Gromos96 model correctly aromatic-Aromatic interaction. For more information I am posting my full NVT.mdb file below. I really appreciate your feedback and help in advance. thank you Rob #include ; ; File 'mdout.mdp' was generated ; ; ; LINES STARTING WITH ';' ARE COMMENTS title = NVT equlibration ; Title of run cpp = /usr/bin/cpp ; location of cpp on linux ; The following lines tell the program the standard locations where to find certain files ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = ; e.g.: -DI_Want_Cookies -DMe_Too define = -DPOSRES ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 5 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 100 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; TEST PARTICLE INSERTION OPTIONS rtpi = 0.05 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 100 nstvout = 100 nstfout = 100 ; Output frequency for energies to log file and energy file nstlog = 100 nstenergy= 100 ; Output frequency and precision for xtc file nstxtcout= 100 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps
[gmx-users] Problems with parallel run
Hi all My apologies for the lack of detail in my previous e-mail. I am trying to run gromacs-4.0.7 for a system that I am studying. I have ran several simulations on serial on my own computer that have to date worked fine. I am now however trying to run the simulations on our local cluster in parallel using mpich-1.2.7 and experiencing some difficulty. Please note that the version of gromacs mentioned above is installed in parallel. Right when I run a short simulation of 500 steps in one two or three nodes the simulations runs fine (takes about 10 seconds) and all the data is written to the log file. However when I increase the nodes to 4 there is no stepwise info written and the simulation does not progress. I realise that this maybe a cluster problem, but if anyone has experienced similar issues I would be grateful of some feedback. Here is the script I use: #!/bin/bash #PBS -N hex #PBS -r n #PBS -q longterm #PBS -l walltime=00:30:00 #PBS -l nodes=4 cd $PBS_O_WORKDIR export P4_GLOBMEMSIZE=1 /usr/local/bin/mpiexec mdrun -s Also here is my path: # Gromacs export GMXLIB=/k/gavin/gromacs-4.0.7-parallel/share/gromacs/top export PATH=$PATH:/k/gavin/gromacs-4.0.7-parallel/bin Cheers Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with the size of freeze groups
Dear Berk, Thanks for your reply, I have just submitted all my files to bugzilla.gromacs.org. I got the bug # 400. Thanks very much Srinivas. On Wed, Mar 3, 2010 at 4:15 AM, Berk Hess g...@hotmail.com wrote: Hi, I don't know exactly what you have done, so currently I can say more than I have done already. Could you please file a bugzilla at bugzilla.gromacs.org and attach all the files required to run grompp? Thanks, Berk -- Date: Tue, 2 Mar 2010 21:11:06 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, Thanks for your previous responses, Can you please let me know if you have any solution for the size of freezing groups? I am still not able to do if i have larger freezing groups. Thanks again for your kind help. srinivas. On Fri, Feb 26, 2010 at 5:37 PM, jampani srinivas jampa...@gmail.comwrote: Dear Berk, I have checked my inputs and tcl scripts that i have used for the selection, i could see that my selection doesn't have any problem. I submitted it again still i am getting the same log file with nrdf 0 for non-freezing group. Please let me know if you want see any of my input files, and help me if you have solution for this problem. Thanks and Regards Srinivas. On Fri, Feb 26, 2010 at 12:39 PM, jampani srinivas jampa...@gmail.comwrote: Dear Berk, I am using VERSION 4.0.5. As you said if there is no problem i should get it correctly, i don't know where it is going wrong. I have written a small script in tcl to use in vmd to get my selections. i will check the script and the selection again. I will let you know my results again. Thanks for your valuable time and kind help. Srinivas. On Fri, Feb 26, 2010 at 12:29 PM, Berk Hess g...@hotmail.com wrote: Hi, Which version of Gromacs are you using? I can't see any issues in the 4.0 code, but some older version might have problems. Berk -- Date: Fri, 26 Feb 2010 12:05:56 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, They are same, freeze and Tmp2 are exactly the same groups. I just put them like that for my convenience, just to avoid confusion in my second email i made it uniform. Thanks Srinivas. On Fri, Feb 26, 2010 at 11:59 AM, Berk Hess g...@hotmail.com wrote: That is what I suspected, by I don't know why this is. Are you really sure you made a temperature coupling group that is exactly the freeze group? This first mdp file you mailed had a different group names for the freeze group and the tcoupl groups. Berk -- Date: Fri, 26 Feb 2010 11:53:49 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, It looks to me some thing is wrong when i change the radius from 35 to 25, herewith i am giving grpopts for both systems + grpopts: (system with 35 A) nrdf: 33141.4 0 ref_t: 300 0 tau_t: 0.1 0.1 + grpopts: (system with 25A) nrdf: 0 0 ref_t: 300 0 tau_t: 0.1 0.1 I think some thing is going wrong when the size of freezing group is increased. I don't know whether my understand is correct or not. Thanks Srinivas. On Fri, Feb 26, 2010 at 11:01 AM, Berk Hess g...@hotmail.com wrote: Ah, but that does not correspond to the mdp options tou mailed. Here there is only one group with 0 degrees of freedom and reference temperature 0. Berk -- Date: Fri, 26 Feb 2010 10:50:13 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org HI Thanks, My log file shows me nrdf: 0 ### grpopts: nrdf: 0 ref_t:0 tau_t: 0 ### Thanks Srinivas. On Fri, Feb 26, 2010 at 10:25 AM, Berk Hess g...@hotmail.com wrote: Hi, Then I have no clue what might be wrong. Have you check nrdf in the log file? Berk -- Date: Fri, 26 Feb 2010 09:54:22 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, Thanks for your response, As you mentioned i have separated t-coupling group for frozen and non-frozen groups, still the result is same. Herewith i am giving my md.mdp file, Can you suggest me if i am missing any options in my md.mdp file? Thanks again Srinivas. md.mdp file +++ title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt
Re: [gmx-users] NVT simulation and mdp file
tekle...@ualberta.ca wrote: Dear Gromacs Users, I have encountered the following issues while I was running my MD simulation. Can anybody comment on what the meaning of these notes are. Is there anything I could do to avoid them. NOTE 2 [file PAP.top, line unknown]: The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. My SOLVENT IS TOLUENE --- the PRODRG gave me a topology file with only one group charge only. That's almost certainly wrong. See, for instance, the PHE side chain in the relevant .rtp entry for a more reasonable charge group setup. If you're using PRODRG defaults, then the charges are probably unsatisfactory, as well. The rationale for the charge group size is summed up here: http://lists.gromacs.org/pipermail/gmx-users/2008-November/038153.html NOTE 1 [file nvt.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. See the literature about this one, as well as the numerous list archive discussions. For initial equilibration, a weak coupling scheme is probably fine, but you can also use V-rescale. Also of interest: http://www.gromacs.org/Documentation/Terminology/Thermostats NOTE 3 [file aminoacids.dat, line 1]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing This all depends on the size of your system, how much of the work is distributed between the real-space Coulombic interaction and PME. In addition to the above notes I have also some questions about the NVT and NPT simulation. 1)I am using toluene as a solvent to simulate my polymer, do I need to use the compressibility of toluene which is 9.2e-5 or the default value 4.5e-5 1/bar. Well, 4.5e-5 corresponds to water, which you aren't using... For NVT, this won't matter since the box is fixed, but for NPT, the compressibility will affect the response of your system to pressure. The differences may be minimal, but if you know the right value, why accept a wrong one? 2)What about the dielectric constant (the dielectric constant for toluene is 2-2.4), but the default value is 80 ( I assume this is for water- am I right). Yes, the default again assumes water as the solvent. 3)Is always rvdw = 1.4 nm for GROMOS96. As a result I have to increase my box size of the solute at the beginning to a min of 2*1.4 =2.8 ( min image convection). Is this the right way to do! At an absolute minimum. Keep in mind that the box vectors will fluctuate under NPT, so if the box decreases even a little bit below 2.8, you will be violating the minimum image convention. 4)I run an NVT simulation to equilibrate my system for 100 ps. When I checked my simulation at the end (successfully completed) I noticed that the shape of my simulation box looks CIRCULAR! some how the rectangular shape looks distorted. What does this tell! Do you guys think something is wrong in my simulation. This could be some visualization artifact, or the components of your system have condensed within the box. Without actually seeing it, it's hard to tell. If you post an image online (Photobucket, etc) then we might get a better sense of what's going on. 5)I included the polar and aromatic hydrogens in my simulation ( ffG43a1.itp – GROMOS96.1 in PRODRG). Does these hydrogen influence my result as the force field is a united atom force field. Or How can I get rid of them if I want. With or without the aromatic hydrogen gave good results ( besides lower computational cost). Does Gromos96 model correctly aromatic-Aromatic interaction. Well, correct is a relative term for all force fields, but you need to follow the prescribed setup of the force field itself, otherwise you can throw it all away. If you lump the hydrogens into the ring carbons and have an uncharged ring, the result will be different than if you have the hydrogens there with a small charge on each C and H. Again, refer to the force field .rtp file for examples. You can also create a better toluene topology by renaming the residue in your coordinate file PHE and trick pdb2gmx: pdb2gmx -f toluene.pdb -missing Then change the mass of the CH2 group (which pdb2gmx thinks is a CB for PHE) to reflect a CH3 group. Make an .itp file out of the resulting .top by removing the unnecessary #includes, [system], and [molecule] directives. Then you don't have to worry about messing with PRODRG. I should note, as well, that this
Re: [gmx-users] Problems with parallel run
This email (as well as the two others) have found their way to the list. No need to post several times! On Wed, Mar 3, 2010 at 12:47, Gavin Melaugh gmelaug...@qub.ac.uk wrote: Hi all My apologies for the lack of detail in my previous e-mail. I am trying to run gromacs-4.0.7 for a system that I am studying. I have ran several simulations on serial on my own computer that have to date worked fine. I am now however trying to run the simulations on our local cluster in parallel using mpich-1.2.7 and experiencing some difficulty. Please note [...] If you would have searched the mailing list for posts with terms like parallel problem, you probably would have found several posts that report people having serious problems with mpich-1.2.x and the advise to use mpich2, openMPI or LAM/MPI instead. Check with the admins of your Cluster which alternative MPI lib is available or have them install one of the suggested. Oliver -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] ethanol bond types
Hello, I am trying to simulate Ethanol in water using OPLSAA. I already tried it with all atoms, but now I want to try it with United atoms for ethanol, i.e. CH3,CH2,OH, and HO in my topology file. I created the topology but I got an error saying 'No bond types', so I checked ffoplsaabon.itp file, and as the error indicated I could not find any bond types. Is there a way for me to determine the bonds? This is my topology file for ethanol: [ moleculetype ] ; Namenrexcl Ethanol 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_068 1EOH CB 1 0 15.035 ; qtot 0 2 opls_081 1EOH CA 2 0.265 14.027 ; qtot 0.265 3 opls_078 1EOH OH 2 -0.715.9994 ; qtot -0.435 4 opls_079 1EOH HO 2 0.435 1.008 ; qtot 0 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 2 3 1 3 4 1 [ pairs ] ; aiaj functc0c1c2c3 1 4 1 [ angles ] ; aiajak functc0c1c2 c3 1 2 3 1 2 3 4 1 [ dihedrals ] ; aiajakal functc0c1 c2c3c4c5 1 2 3 4 3 I checked one of the paper that has been published using the same parameters as follows: Table 1. Potential Parameters and Molecular Geometries of OPLS-UA and SPC/E qa atom or group ?, Å , kJ/mol OPLS R13.905 0.73220.000 R23.905 0.49370.265 -0.700 O 3.070 0.7113 H 0.000 0.0.435 I would really appreciate some suggestions, on how I should tackle the error. Thanks Nisha P -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems with parallel run
Hi Oliver Thanks very much. Sorry about the other two e-mails that was a mistake, I had checked the list after I sent the first one and it wasn't on so I thought it wasn't received. I was reading many of those posts today and did realise that there were problems with mpich-1.2.x but they seemed to be for earlier versions of gromacs and it was on this point that I was unsure. Thanks anyway for providing some insight on the matter. Cheers Gavin Oliver Stueker wrote: This email (as well as the two others) have found their way to the list. No need to post several times! On Wed, Mar 3, 2010 at 12:47, Gavin Melaugh gmelaug...@qub.ac.uk wrote: Hi all My apologies for the lack of detail in my previous e-mail. I am trying to run gromacs-4.0.7 for a system that I am studying. I have ran several simulations on serial on my own computer that have to date worked fine. I am now however trying to run the simulations on our local cluster in parallel using mpich-1.2.7 and experiencing some difficulty. Please note [...] If you would have searched the mailing list for posts with terms like parallel problem, you probably would have found several posts that report people having serious problems with mpich-1.2.x and the advise to use mpich2, openMPI or LAM/MPI instead. Check with the admins of your Cluster which alternative MPI lib is available or have them install one of the suggested. Oliver -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ethanol bond types
On 3/3/10 8:14 PM, nishap.pa...@utoronto.ca wrote: Hello, I am trying to simulate Ethanol in water using OPLSAA. I already tried it with all atoms, but now I want to try it with United atoms for ethanol, i.e. CH3,CH2,OH, and HO in my topology file. I created the topology but I got an error saying 'No bond types', so I checked ffoplsaabon.itp file, and as the error indicated I could not find any bond types. Is there a way for me to determine the bonds? This is my topology file for ethanol: [ moleculetype ] ; Namenrexcl Ethanol 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_068 1EOH CB 1 0 15.035 ; qtot 0 2 opls_081 1EOH CA 2 0.265 14.027 ; qtot 0.265 3 opls_078 1EOH OH 2 -0.715.9994 ; qtot -0.435 4 opls_079 1EOH HO 2 0.435 1.008 ; qtot 0 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 2 3 1 3 4 1 [ pairs ] ; aiaj functc0c1c2c3 1 4 1 [ angles ] ; aiajak functc0c1c2 c3 1 2 3 1 2 3 4 1 [ dihedrals ] ; aiajakal functc0c1 c2c3c4c5 1 2 3 4 3 I checked one of the paper that has been published using the same parameters as follows: Table 1. Potential Parameters and Molecular Geometries of OPLS-UA and SPC/E qa atom or group ?, Å , kJ/mol OPLS R13.905 0.73220.000 R23.905 0.49370.265 -0.700 O 3.070 0.7113 H 0.000 0.0.435 I would really appreciate some suggestions, on how I should tackle the error. Thanks Nisha P The united atom parameters are really leftovers from long past. Jorgensen published his first all-atom alcohol simulations in 1988 IIRC. There is a methanol paper from 1983. Just search literature for Jorgensen, methanol ethanol and it will show up. Then you will to type in the parameters yourself, see chapter 5. -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://xray.bmc.uu.se/~spoel -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: GROMACS PME on BLUEGENE
On 4/03/2010 3:54 AM, Xevi Biarnes Fontal (SISSA) wrote: Dear Mark, I found a topic in the gromacs-users mailing list regarding your troubles in running gromacs with PME on BlueGene/P (http://lists.gromacs.org/pipermail/gmx-users/2009-June/042421.html) did you solve the problem? Please keep such discussions on the mailing list. I might not have the expertise or time to help, and if someone can help, the answer should be archived for all to find. Imagine if you'd not being able to find anything with searches :-) I am now facing exactly the same problem. If I turn on PME I get the execution stacked and a core file written out. If I don't request for PME (i.e. Cut-Off) the execution runs without problems. I wasn't having any problem with BlueGene, if you read that email exchange carefully. Jakob was. He apparently never shared his solution, if any. Try running on one CPU (mdrun -np 1 -exe blah -args blahblah) to see if the problem is generic, or parallel-related. Read in your BlueGene documentation how to use addr2line to probe the stack dump. You'll need to compile a version of mdrun with debugging enabled (add -g to any CFLAGS=... on your configure command line) for this detective work to succeed. That will tell you the function and line number where the problem occurs, which will likely lead to a solution. Complain to IBM that this is a 1960s solution :) Obviously, once it's fixed, get rid of the debugging version. If you solved the problem, can you tell me which steps did you follow. I compiled gromacs-4.0.7 with FFTW3.1.2 for the backend and with a modified version of the same libraries for the frontend. (I am using the configure options explained in http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions/GROMACS_on_BlueGene) If you're using BG/P, note Puetz's comments there about fixing MPI libraries and such. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] External forces
Hi all, Can anyone tell me how I can impart external forces on a system - say I have a water droplet placed on a tilted polymer surface. With the application of the force, the droplet should flow. - Rohit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] External forces
ROHIT MALSHE wrote: Hi all, Can anyone tell me how I can impart external forces on a system - say I have a water droplet placed on a tilted polymer surface. With the application of the force, the droplet should flow. That's what the pull code is for. -Justin - Rohit -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] NVT simulation and mdp file
tekle...@ualberta.ca wrote: Dear Justin, I really appreciate your help and feedback. once again thank you for your time. This could be some visualization artifact, or the components of your system have condensed within the box. Without actually seeing it, it's hard to tell. If you post an image online (Photobucket, etc) then we might get a better sense of what's going on. Here is my .gro file taht looks like condensed. Attached please find the NVT.gro file or the images in .jpeg file format Please note that this is not what I suggested you do. Posting images online (not to the list) is a far better method. Users who subscribe to the list in digest format will not get these attachments, and thus you alienate others who might be able to help you. Also, for the security-conscious, download attachments is not always preferable. It seems pretty clear from what's going on that your system is simply condensing, so your initial configuration placed all the molecules too far apart (at too low of a density). Display the box vectors in VMD and you will see exactly what's going on: (Tk console) package require pbctools pbc box -Justin Best, Rob Quoting Justin A. Lemkul jalem...@vt.edu: tekle...@ualberta.ca wrote: Dear Gromacs Users, I have encountered the following issues while I was running my MD simulation. Can anybody comment on what the meaning of these notes are. Is there anything I could do to avoid them. NOTE 2 [file PAP.top, line unknown]: The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. My SOLVENT IS TOLUENE --- the PRODRG gave me a topology file with only one group charge only. That's almost certainly wrong. See, for instance, the PHE side chain in the relevant .rtp entry for a more reasonable charge group setup. If you're using PRODRG defaults, then the charges are probably unsatisfactory, as well. The rationale for the charge group size is summed up here: http://lists.gromacs.org/pipermail/gmx-users/2008-November/038153.html NOTE 1 [file nvt.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. See the literature about this one, as well as the numerous list archive discussions. For initial equilibration, a weak coupling scheme is probably fine, but you can also use V-rescale. Also of interest: http://www.gromacs.org/Documentation/Terminology/Thermostats NOTE 3 [file aminoacids.dat, line 1]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing This all depends on the size of your system, how much of the work is distributed between the real-space Coulombic interaction and PME. In addition to the above notes I have also some questions about the NVT and NPT simulation. 1)I am using toluene as a solvent to simulate my polymer, do I need to use the compressibility of toluene which is 9.2e-5 or the default value 4.5e-5 1/bar. Well, 4.5e-5 corresponds to water, which you aren't using... For NVT, this won't matter since the box is fixed, but for NPT, the compressibility will affect the response of your system to pressure. The differences may be minimal, but if you know the right value, why accept a wrong one? 2)What about the dielectric constant (the dielectric constant for toluene is 2-2.4), but the default value is 80 ( I assume this is for water- am I right). Yes, the default again assumes water as the solvent. 3)Is always rvdw = 1.4 nm for GROMOS96. As a result I have to increase my box size of the solute at the beginning to a min of 2*1.4 =2.8 ( min image convection). Is this the right way to do! At an absolute minimum. Keep in mind that the box vectors will fluctuate under NPT, so if the box decreases even a little bit below 2.8, you will be violating the minimum image convention. 4)I run an NVT simulation to equilibrate my system for 100 ps. When I checked my simulation at the end (successfully completed) I noticed that the shape of my simulation box looks CIRCULAR! some how the rectangular shape looks distorted. What does this tell! Do you guys think something is wrong in my simulation. This could be some visualization artifact, or the components of your system have condensed within the box. Without actually seeing it, it's hard to tell. If you post an image online (Photobucket, etc) then we might get a better sense of what's going on. 5)I included the
Re: [gmx-users] gromacs memory usage
Hi Roland, I was using 32 nodes with 8 cores, each with 16 Gb memory. The system was about 154 M particles. This should be feasible according to the numbers. Assuming that it takes 50bytes per atoms and 1.76 KB per atom per core then Masternode - (50*154 M + 8*1.06)bytes ~ 16GB (There is no leverage here) All other nodes 8*1.06 ~ 8.5 GB I am planning to try the same run on 64 nodes with 8 cores each again but not until i am a little more confident. The problem is if gromacs crashes due to memory it makes the nodes to hang and people have to recycle the power supply. Thank you, amit On Wed, Mar 3, 2010 at 7:34 AM, Roland Schulz rol...@utk.edu wrote: Hi, ok then it is compiled in 64bit. You didn't say how many cores each node has and on how many nodes you want to run. Roland On Wed, Mar 3, 2010 at 4:32 AM, Amit Choubey kgp.a...@gmail.com wrote: Hi Roland, It says gromacs/4.0.5/bin/mdrun_mpi: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), for GNU/Linux 2.6.9, not stripped On Tue, Mar 2, 2010 at 10:34 PM, Roland Schulz rol...@utk.edu wrote: Amit, try the full line (with the file) Roland On Wed, Mar 3, 2010 at 1:22 AM, Amit Choubey kgp.a...@gmail.com wrote: Hi Roland I tried 'which mdrun' but it only gives the path name of installation. Is there any other way to know if the installation is 64 bit ot not? Thank you, Amit On Tue, Mar 2, 2010 at 10:03 PM, Roland Schulz rol...@utk.edu wrote: Hi, do: file `which mdrun` and it should give: /usr/bin/mdrun: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.15, stripped If it is not 64 you need to compile with 64 and have a 64bit kernel. Since you asked before about 2GB large files this might indeed be your problem. Roland On Wed, Mar 3, 2010 at 12:48 AM, Amit Choubey kgp.a...@gmail.comwrote: Hi Tsjerk, I tried to do a test run based on the presentation. But there was a memory related error (I had given a leverage of more than 2 GB). I did not understand the 64 bit issue, could you let me know wheres the documentation? I need to look into that. Thank you, amit On Tue, Mar 2, 2010 at 9:14 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Amit, I think the presentation gives right what you want: a rough estimate. Now as Berk pointed out, to allocate more than 2GB of memory, you need to compile in 64bit. Then, if you want to have a real feel for the memory usage, there's no other way than trying. But fortunately, the memory requirements of a (very) long simulation are equal to that of a very short one, so it doesn't need to cost much time. Cheers, Tsjerk On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey kgp.a...@gmail.com wrote: Hi Mark, Yes thats one way to go about it. But it would have been great if i could get a rough estimation. Thank you. amit On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 3/03/2010 12:53 PM, Amit Choubey wrote: Hi Mark, I quoted the memory usage requirements from a presentation by Berk Hess, Following is the link to it http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf l. In that presentation on pg 27,28 Berk does talk about memory usage but then I am not sure if he referred to any other specific thing. My system only contains SPC water. I want Berendsen T coupling and Coulomb interaction with Reaction Field. I just want a rough estimate of how big of a system of water can be simulated on our super computers. Try increasingly large systems until it runs out of memory. There's your answer. Mark On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: - Original Message - From: Amit Choubey kgp.a...@gmail.com mailto: kgp.a...@gmail.com Date: Saturday, February 27, 2010 10:17 Subject: Re: [gmx-users] gromacs memory usage To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Hi Mark, We have few nodes with 64 GB memory and many other with 16 GB of memory. I am attempting a simulation of around 100 M atoms. Well, try some smaller systems and work upwards to see if you have a limit in practice. 50K atoms can be run in less than 32GB over 64 processors. You didn't say whether your simulation system can run on 1 processor... if it does, then you can be sure the problem really is related to parallelism. I did find some document which says one need (50bytes)*NATOMS on master node, also one needs (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute nodes. Is this true? In general, no. It will vary with the simulation algorithm you're
[gmx-users] g_mindist periodic boundary condition
Hi Gromacs users, I was trying to compute minimum distance between groups in a cubic water box with g_mindist using periodic boundary condition. In order to test this, I added one more atom which is far away from any of the other atoms in the pdb file. The mindist between that atom and all the waters were computed. The output of g_mindist is 3.089281e+00. (the unit is nm, right?) The manual shows that pbc is one of the option of g_mindist, but isn't the default yes? I even tried with -pbc in the command, still did not work. Can anyone tell me how to turn on PBC in g_mindist? Thanks Dian -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs memory usage
Hi, a couple of points: 1) you will need some additional memory for the system, MPI, the binary, - how much this is does not depend on GROMACS (ask e.g. your sys-admin) 2) you might want to try to run only 1 rank on the first node (how to do this depends on your MPI implementation and should be asked on the specific MPI list) 3) By setting limits (e.g. ulimit with bash) you can prevent the system to freeze (again ask you sysadmin about how to use limits) 4) You can compile GROMACS with CFLAGS=-DPRINT_ALLOC_KB and it gives debug information about the memory usage. This can be used to verify the my/Berk's numbers Roland On Wed, Mar 3, 2010 at 7:15 PM, Amit Choubey kgp.a...@gmail.com wrote: Hi Roland, I was using 32 nodes with 8 cores, each with 16 Gb memory. The system was about 154 M particles. This should be feasible according to the numbers. Assuming that it takes 50bytes per atoms and 1.76 KB per atom per core then Masternode - (50*154 M + 8*1.06)bytes ~ 16GB (There is no leverage here) All other nodes 8*1.06 ~ 8.5 GB I am planning to try the same run on 64 nodes with 8 cores each again but not until i am a little more confident. The problem is if gromacs crashes due to memory it makes the nodes to hang and people have to recycle the power supply. Thank you, amit On Wed, Mar 3, 2010 at 7:34 AM, Roland Schulz rol...@utk.edu wrote: Hi, ok then it is compiled in 64bit. You didn't say how many cores each node has and on how many nodes you want to run. Roland On Wed, Mar 3, 2010 at 4:32 AM, Amit Choubey kgp.a...@gmail.com wrote: Hi Roland, It says gromacs/4.0.5/bin/mdrun_mpi: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), for GNU/Linux 2.6.9, not stripped On Tue, Mar 2, 2010 at 10:34 PM, Roland Schulz rol...@utk.edu wrote: Amit, try the full line (with the file) Roland On Wed, Mar 3, 2010 at 1:22 AM, Amit Choubey kgp.a...@gmail.comwrote: Hi Roland I tried 'which mdrun' but it only gives the path name of installation. Is there any other way to know if the installation is 64 bit ot not? Thank you, Amit On Tue, Mar 2, 2010 at 10:03 PM, Roland Schulz rol...@utk.edu wrote: Hi, do: file `which mdrun` and it should give: /usr/bin/mdrun: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.15, stripped If it is not 64 you need to compile with 64 and have a 64bit kernel. Since you asked before about 2GB large files this might indeed be your problem. Roland On Wed, Mar 3, 2010 at 12:48 AM, Amit Choubey kgp.a...@gmail.comwrote: Hi Tsjerk, I tried to do a test run based on the presentation. But there was a memory related error (I had given a leverage of more than 2 GB). I did not understand the 64 bit issue, could you let me know wheres the documentation? I need to look into that. Thank you, amit On Tue, Mar 2, 2010 at 9:14 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Amit, I think the presentation gives right what you want: a rough estimate. Now as Berk pointed out, to allocate more than 2GB of memory, you need to compile in 64bit. Then, if you want to have a real feel for the memory usage, there's no other way than trying. But fortunately, the memory requirements of a (very) long simulation are equal to that of a very short one, so it doesn't need to cost much time. Cheers, Tsjerk On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey kgp.a...@gmail.com wrote: Hi Mark, Yes thats one way to go about it. But it would have been great if i could get a rough estimation. Thank you. amit On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 3/03/2010 12:53 PM, Amit Choubey wrote: Hi Mark, I quoted the memory usage requirements from a presentation by Berk Hess, Following is the link to it http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf l. In that presentation on pg 27,28 Berk does talk about memory usage but then I am not sure if he referred to any other specific thing. My system only contains SPC water. I want Berendsen T coupling and Coulomb interaction with Reaction Field. I just want a rough estimate of how big of a system of water can be simulated on our super computers. Try increasingly large systems until it runs out of memory. There's your answer. Mark On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: - Original Message - From: Amit Choubey kgp.a...@gmail.com mailto: kgp.a...@gmail.com Date: Saturday, February 27, 2010 10:17 Subject: Re: [gmx-users] gromacs memory usage To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Hi Mark, We have few nodes with
Re: [gmx-users] g_mindist periodic boundary condition
On 4/03/2010 11:30 AM, Dian Jiao wrote: Hi Gromacs users, I was trying to compute minimum distance between groups in a cubic water box with g_mindist using periodic boundary condition. In order to test this, I added one more atom which is far away from any of the other atoms in the pdb file. The mindist between that atom and all the waters were computed. The output of g_mindist is 3.089281e+00. (the unit is nm, right?) You haven't said how big your box is, or how far far away is, so we can't tell whether you think 3nm is too big, too small, etc. The manual shows that pbc is one of the option of g_mindist, but isn't the default yes? I even tried with -pbc in the command, still did not work. Can anyone tell me how to turn on PBC in g_mindist? See g_mindist -h. The -pbc flag turns PBC on, -nopbc turns it off. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs memory usage
On 4/03/2010 11:15 AM, Amit Choubey wrote: Hi Roland, I was using 32 nodes with 8 cores, each with 16 Gb memory. The system was about 154 M particles. This should be feasible according to the numbers. Assuming that it takes 50bytes per atoms and 1.76 KB per atom per core then Masternode - (50*154 M + 8*1.06)bytes ~ 16GB (There is no leverage here) All other nodes 8*1.06 ~ 8.5 GB I am planning to try the same run on 64 nodes with 8 cores each again but not until i am a little more confident. The problem is if gromacs crashes due to memory it makes the nodes to hang and people have to recycle the power supply. Your sysadmins should be able to come up with a better solution than that. Not doing so just makes work for them detecting and rebooting things by hand for the next 5 years. The traditional approach is to use virtual memory on disk. Now the calculation will run, but will be slow when accessing less-frequently used memory. In GROMACS, that will only be those all-atom arrays on the master process, which probably only get accessed during input, DD and output phases, which are already slow. At the very least, they need a malloc library that doesn't lead to a system hang. Mark On Wed, Mar 3, 2010 at 7:34 AM, Roland Schulz rol...@utk.edu mailto:rol...@utk.edu wrote: Hi, ok then it is compiled in 64bit. You didn't say how many cores each node has and on how many nodes you want to run. Roland On Wed, Mar 3, 2010 at 4:32 AM, Amit Choubey kgp.a...@gmail.com mailto:kgp.a...@gmail.com wrote: Hi Roland, It says gromacs/4.0.5/bin/mdrun_mpi: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), for GNU/Linux 2.6.9, not stripped On Tue, Mar 2, 2010 at 10:34 PM, Roland Schulz rol...@utk.edu mailto:rol...@utk.edu wrote: Amit, try the full line (with the file) Roland On Wed, Mar 3, 2010 at 1:22 AM, Amit Choubey kgp.a...@gmail.com mailto:kgp.a...@gmail.com wrote: Hi Roland I tried 'which mdrun' but it only gives the path name of installation. Is there any other way to know if the installation is 64 bit ot not? Thank you, Amit On Tue, Mar 2, 2010 at 10:03 PM, Roland Schulz rol...@utk.edu mailto:rol...@utk.edu wrote: Hi, do: file `which mdrun` and it should give: /usr/bin/mdrun: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.15, stripped If it is not 64 you need to compile with 64 and have a 64bit kernel. Since you asked before about 2GB large files this might indeed be your problem. Roland On Wed, Mar 3, 2010 at 12:48 AM, Amit Choubey kgp.a...@gmail.com mailto:kgp.a...@gmail.com wrote: Hi Tsjerk, I tried to do a test run based on the presentation. But there was a memory related error (I had given a leverage of more than 2 GB). I did not understand the 64 bit issue, could you let me know wheres the documentation? I need to look into that. Thank you, amit On Tue, Mar 2, 2010 at 9:14 PM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Amit, I think the presentation gives right what you want: a rough estimate. Now as Berk pointed out, to allocate more than 2GB of memory, you need to compile in 64bit. Then, if you want to have a real feel for the memory usage, there's no other way than trying. But fortunately, the memory requirements of a (very) long simulation are equal to that of a very short one, so it doesn't need to cost much time. Cheers, Tsjerk On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey kgp.a...@gmail.com mailto:kgp.a...@gmail.com wrote: Hi Mark,
Re: [gmx-users] g_mindist periodic boundary condition
The box is 24X24X24 (Angstrom). The dummy atom I added at the end is about 31 A away from the closest water in the box. But if it is periodic, shouldn't there be waters near the dummy too? On Wed, Mar 3, 2010 at 10:29 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/03/2010 11:30 AM, Dian Jiao wrote: Hi Gromacs users, I was trying to compute minimum distance between groups in a cubic water box with g_mindist using periodic boundary condition. In order to test this, I added one more atom which is far away from any of the other atoms in the pdb file. The mindist between that atom and all the waters were computed. The output of g_mindist is 3.089281e+00. (the unit is nm, right?) You haven't said how big your box is, or how far far away is, so we can't tell whether you think 3nm is too big, too small, etc. The manual shows that pbc is one of the option of g_mindist, but isn't the default yes? I even tried with -pbc in the command, still did not work. Can anyone tell me how to turn on PBC in g_mindist? See g_mindist -h. The -pbc flag turns PBC on, -nopbc turns it off. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_mindist periodic boundary condition
Hi Dian, Which version of gromacs are you using? Can you assert that the pdb file has the correct box? It should have a line starting with CRYST1 (grep ^CRYST1 file.pdb). Some versions of gromacs (3.3.2 I think) didn't write the CRYST1 record, and thus disallow PBC related operations. Cheers, Tsjerk On Thu, Mar 4, 2010 at 8:08 AM, Dian Jiao oscarj...@gmail.com wrote: The box is 24X24X24 (Angstrom). The dummy atom I added at the end is about 31 A away from the closest water in the box. But if it is periodic, shouldn't there be waters near the dummy too? On Wed, Mar 3, 2010 at 10:29 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 4/03/2010 11:30 AM, Dian Jiao wrote: Hi Gromacs users, I was trying to compute minimum distance between groups in a cubic water box with g_mindist using periodic boundary condition. In order to test this, I added one more atom which is far away from any of the other atoms in the pdb file. The mindist between that atom and all the waters were computed. The output of g_mindist is 3.089281e+00. (the unit is nm, right?) You haven't said how big your box is, or how far far away is, so we can't tell whether you think 3nm is too big, too small, etc. The manual shows that pbc is one of the option of g_mindist, but isn't the default yes? I even tried with -pbc in the command, still did not work. Can anyone tell me how to turn on PBC in g_mindist? See g_mindist -h. The -pbc flag turns PBC on, -nopbc turns it off. Mark -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs memory usage
Hi Looks like your system simply runs out of memory. So power cycling nodes isnt needed. If your cluster runs linux then it already has OOM Killer that will kill processes that runs out of memory. Also having swap on nodes is a good idea even with huge amount of memory. Memory usage for mpi processes will strongly depend on mpi implentation because some of them are usualy caching slave process memory (like usualy do mvapich2) So can you provide info about youre cluster setup. OS version (including kernel version) uname -a mpi version mpirun --version or mpiexec --version also compiler version that was used for compiling gromacs On Четверг 04 марта 2010 03:15:53 Amit Choubey wrote: Hi Roland, I was using 32 nodes with 8 cores, each with 16 Gb memory. The system was about 154 M particles. This should be feasible according to the numbers. Assuming that it takes 50bytes per atoms and 1.76 KB per atom per core then Masternode - (50*154 M + 8*1.06)bytes ~ 16GB (There is no leverage here) All other nodes 8*1.06 ~ 8.5 GB I am planning to try the same run on 64 nodes with 8 cores each again but not until i am a little more confident. The problem is if gromacs crashes due to memory it makes the nodes to hang and people have to recycle the power supply. Thank you, -- Best Regards, Alexey 'Alexxy' Shvetsov Petersburg Nuclear Physics Institute, Russia Department of Molecular and Radiation Biophysics Gentoo Team Ru Gentoo Linux Dev mailto:alexx...@gmail.com mailto:ale...@gentoo.org mailto:ale...@omrb.pnpi.spb.ru signature.asc Description: This is a digitally signed message part. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
