Re: [gmx-users] gmx_ana_selcolletion_t definition

Hello again, I've talked to my adviser and we agreed to install version 5.1. I'll take a look in the documentation and try to work on it. Murilo. 2016-07-13 10:19 GMT-06:00 MURILO GABARDO KRAMAR < murilokra...@alunos.utfpr.edu.br>: > Hello Mark, > > Thanks for you answer, > > My concern about

Re: [gmx-users] periodic boundary conditions

Any other comment on this? :-) On Wed, Jul 13, 2016 at 9:50 AM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Hi Mark, > > Thanks for your reply. > > The 6 around 1 setup is also periodic. > > I understand this. However, we can argue the same for 6-1 system as well. > Right? > > If

Re: [gmx-users] Correct .mdp file for Amber99SB-ILDN ff implementation in Gromacs

On 7/14/16 12:40 PM, Mohsen Ramezanpour wrote: Thanks Joao and Justin for your comments, As Justin mentioned, I followed the original articles on this force field. However, I was not sure if the same parameters can be transferred to Gromacs or not. The cutoffs are straightforward to get

Re: [gmx-users] PRACE benchmarks

Few cents on this. On our cluster with well configured OpenMPI 1.8.8, 1.10.2 and 1.10.3 (and 2.0.0 in testing) gromacs-5.1.2 runs smoothly with the above mentioned openmpi versions using the same prace benchmarks case (CaseB). Performance with these openmpi versions (for a 6 minutes maxh,

Re: [gmx-users] Correct .mdp file for Amber99SB-ILDN ff implementation in Gromacs

Thanks Joao and Justin for your comments, As Justin mentioned, I followed the original articles on this force field. However, I was not sure if the same parameters can be transferred to Gromacs or not. The only thing different was the initial temperature of 50K and increasing it to 310 K through

Re: [gmx-users] GPU Not Being Utilized during mdrun

I'm currently running a simple 1ns calculation with 500,000 steps with dt = 2fs and structures being stored every 10ps. On Thu, Jul 14, 2016 at 11:31 AM, Smith, Micholas D. wrote: > Quick question, what is your integration stepsize? > > === > Micholas Dean

Re: [gmx-users] GPU Not Being Utilized during mdrun

Quick question, what is your integration stepsize? === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From:

[gmx-users] Supercomputing facility

Hello Users and experts We are going to create an account for a supercomputing facility. They have asked to fill a form to initiate the process. I am confused about certain terms as I belong to biology background. Please help me with these specific terms and what should I fill in to get good

[gmx-users] Questions about OPLS force fields

Hi, I am creating a topology for a molecule that is not defined by OPLS. I have some questions that I want to ask: 1. What is bondtype and ptype in ffnonbonded.itp? 2. If I use the Buckingham potential to define nonbonded interactions between atom A and atom B, does this potential apply to all

Re: [gmx-users] PRACE benchmarks

Hi, Any MPI-1.1 conformant implementation is great. The only time GROMACS has problems is when the MPI library does... OpenMPI 1.8.6 leaks memory. 1.8.10 we use locally. Mark On Thu, Jul 14, 2016 at 12:45 PM Adam Huffman wrote: > Hi Mark, > > Hmm. Other applications

Re: [gmx-users] Supercomputing facility

Hi Suniba, assuming that # 5 is GROMACS, then # 2-4 are the required dependencies to have GROMACS running, # 8 is parallel and # 9 is Y. all the other questions refer to the allocation size and the best answer is usually bigger is better. In practice, the largest possible size of the allocation

Re: [gmx-users] truncating LJ potentials

Hi, I decided to test this for a system of sodium and chloride ions (based on http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf ): Guyana Rwanda Oman Macau Angola Cameroon Senegal 8 1NA Na1 0.131 0.116 0.051 2NA Na2 0.137 0.111 0.047 3NA

Re: [gmx-users] GPU Not Being Utilized during mdrun

Hi, If mdrun claims it's using the GPU and you see no errors (and results look reasonable), the GPU is likely being used. That nvidia-smi is not showing it is admittedly strange. However, this truncated log output does not confirm much, e.g. it does not show the performance table and the final

Re: [gmx-users] PRACE benchmarks

Hi Mark, Hmm. Other applications have been working with OpenMPI, but that doesn't invalidate your point. Is there a particular implementation you recommend for GROMACS? Cheers, Adam On Thu, Jul 14, 2016 at 11:00 AM, Mark Abraham wrote: > Hi, > > Looks like your MPI

Re: [gmx-users] Using ATB to generate valid topologies

Tks for the references. For the record, here are the references for ATB: DOI: 10.1021/ct200196m DOI:10.1089/cmb.2012.0239 DOI:10.1007/s10822-014-9713-7 X- >

[gmx-users] Read from XTC file

Dear all, Is there any way to read trajectory using a FORTRAN 90 code directly from .xtc or .trr file? I am working on a trajectory for a protein with a total run time of 1 ns with 5 fs resolution. Converting the .xtc file to .gro format is producing a huge amount of data. So I intend to bypass

Re: [gmx-users] Correct .mdp file for Amber99SB-ILDN ff implementation in Gromacs

> I was wondering if I should modify any terms because of using Gromacs package? It's good practice to set your key parameters as close as possible to theirs. I am not familiar with Desmond, but I assume many of its parameters have similar counterparts in Gromacs. If you plan on (significantly)

Re: [gmx-users] [pairs] vs [exclusions]

Hi Mark, thanks for the elaborate answer. If [pairs] are considered bonded interactions it's perfectly clear. Peter On 13/07/16 17:24, Mark Abraham wrote: > Hi, > > Maybe I missed the point earlier, but as e.g. 5.4.4 Exclusions section of > PDF reference manual says: > > "Extra exclusions

Re: [gmx-users] PRACE benchmarks

Hi, Looks like your MPI setup is broken. So far, I have only heard of people having problems when using OpenMPI 1.10.x, even the latest patch release. Mark On Thu, Jul 14, 2016 at 11:52 AM Adam Huffman wrote: > Hello > > I've been trying to run the PRACE benchmarks on

[gmx-users] PRACE benchmarks

Hello I've been trying to run the PRACE benchmarks on a new cluster: http://www.prace-ri.eu/ueabs/#GROMACS and this is the command-line I've been running: mpirun --mca plm_base_verbose 10 --debug-daemons gmx_mpi mdrun -s ion_channel.tpr -maxh 0.50 -resethway -noconfout -nsteps 1 -g

[gmx-users] electron density by gmx density

Hello Users, I was wandering how can we calculate the electron density with the help of gmx density. how to write the " -ei [<.dat>] (electrons.dat) " Regards, Amit Behera -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. --

Re: [gmx-users] electron density by gmx density

On 7/14/16 6:27 AM, amitbe...@chemeng.iisc.ernet.in wrote: Hello Users, I was wandering how can we calculate the electron density with the help of gmx density. how to write the " -ei [<.dat>] (electrons.dat) " There is an example in the help information. -Justin --

Re: [gmx-users] temperature of a single water molecule

On 7/14/16 1:48 AM, Ali Mohyeddin wrote: Dear all, I am going to calculate the temperature of single water molecule around a protein by writing a simple script to calculate the temperature from what "trjconv" command prints out: mass vx vy vz 2SOL OW 16 0.2789 -0.4959 0.8134 2SOL HW1 1

Re: [gmx-users] Read from XTC file

Hi, check http://manual.gromacs.org/online/xtc.html and http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library They provide standalone library to compile, and examples for C and Fortran. But I never tried it and apparently it was last updated 2 years ago, I hope it can still

[gmx-users] GPU Not Being Utilized during mdrun

Hello After building GROMACS with GPU support and running some simple MD, I am only getting ~20ns/day (which is what I would expect to get out of my i7-6700k cpu only. My machine currently has a 1080 GTX in it, which should even on moderately large systems, be getting ~100ns/day) I've tried

Re: [gmx-users] GPU Not Being Utilized during mdrun

Szilard You are correct; I misspoke. It appears that the GPU is doing *something*, but I it would seem it is severely under performing (near the point where its basically doing nothing). the entire log, not just parts, in particular we want to see the > header, perf table >