Re: [gmx-users] Can't locate state.cpt for gmx mdrun

On 7/7/17 8:00 PM, Yonatan Zelnik wrote: Hello, I am running an energy minimization script that works quite well, except that I can't find any of the checkpoint files that mdrun is supposed to provide. I've been looking through the docs for a while, and I can't seem to find a reason. I have

[gmx-users] Can't locate state.cpt for gmx mdrun

Hello, I am running an energy minimization script that works quite well, except that I can't find any of the checkpoint files that mdrun is supposed to provide. I've been looking through the docs for a while, and I can't seem to find a reason. I have tried the script on multiple systems, and

Re: [gmx-users] Gromacs installation fails in CentOS 6.5

Good that it worked out. You might have changes something in your environment (path?) perhaps between last time and now. On Fri, Jul 7, 2017 at 10:57 PM, Seyed Mostafa Razavi wrote: > Strangely enough, I could install this time,and I do not know why. I > followed exact

Re: [gmx-users] Gromacs installation fails in CentOS 6.5

Strangely enough, I could install this time,and I do not know why. I followed exact same procedure except running make VERBOSE=1 Btw, here is the libgromacs_LIB_DEPENDS line in CMakeCache.txt if you want to know: libgromacs_LIB_DEPENDS:STATIC=general;/usr/lib64/libz.so;gen

[gmx-users] problem: gromacs run on gpu

*Dear Nikhil and Szilárd,* Thanks for your answers. I want to use only one of GPUs (for example ID =1). Should I use option -gpu_id 1? Information of my system hardware is as follows: Running on 1 node with total 96 cores, 192 logical cores, 3 compatible GPUs Hardware detected on host

Re: [gmx-users] Gromacs installation fails in CentOS 6.5

Strange. That means the GROAMCS build system somehow does not get the final link command right. Without investigating deeper, I'm not sure what would be the solution. I'd look a the actual link command that fails (make VERBOSE=1) and try to see what and why is missing. BTW, cmake should know

Re: [gmx-users] Gromacs installation fails in CentOS 6.5

Here is what I did: $ gcc -o omp_helloc -fopenmp omp_hello.c $ ./omp_helloc Hello World from thread = 0 Number of threads = 4 Hello World from thread = 3 Hello World from thread = 1 Hello World from thread = 2 Thank you, S. Mostafa Razavi On Fri, Jul 7, 2017 at 9:12 AM, Szilárd Páll

[gmx-users] Problem reading pdb files

Hi all, I have two pdb files extracted from two trajectories of same compound but starting from two different configurations. I wanted to combined the two trajectories but I faced a broken structures behaviour while combining the two ensembles. I just attached two first frames of each

Re: [gmx-users] Acetonitrile with CHARMM ff

On 7/7/17 10:11 AM, Sonia Milena Aguilera Segura wrote: Dear Justin, Thank you very much for your answer. I tried both approaches: erasing the dihedral from the topology (first approach) and modifying the ffbonded.itp as described in the previous mail, without adding any improper (second

Re: [gmx-users] protein protein interaction: side chain contribution

On 7/7/17 5:34 AM, Tushar Ranjan Moharana wrote: Hi Justin, Thanks a lot for the advice. It looks like I had put one atom in the wrong index group. After correction my results looks as follows: Energy Average Err.Est. RMSD Tot-Drift

Re: [gmx-users] Generating GROMACS input file from the GAMESS output file

On 7/6/17 10:45 PM, 조영래 wrote: Hi gmx users~ I would like to generate *.gro *itp file about one atom for MD simulation. So I calculated Fe metal atom using GAMESS program. -- FE.inp FE.dat FE.log -- How do I make

Re: [gmx-users] Acetonitrile with CHARMM ff

Dear Justin, Thank you very much for your answer. I tried both approaches: erasing the dihedral from the topology (first approach) and modifying the ffbonded.itp as described in the previous mail, without adding any improper (second approach). I ran a minimization, 200 ps NVT, 200 ps NPT, and

Re: [gmx-users] Hardware for GROMACS

Raman, First, please please have a look at the documentation and check out the relevant GROMACS papers (http://www.gromacs.org/Gromacs_papers), in particular http://dx.doi.org/10.1002/jcc.24030 On Tue, Jul 4, 2017 at 5:56 PM, Raman Preet Singh < ramanpreetsi...@hotmail.com> wrote: > Hello, > >

Re: [gmx-users] problem: gromacs run on gpu

You've got a pretty strange beast there with 4 CPU sockets 24 cores each, one very fast GPU and two rather slow ones (about 3x slower than the first). If you want to do a single run on this machine, I suggest trying to partition the rank across the GPUs so that you get a decent balance, e.g. you

Re: [gmx-users] Gromacs installation fails in CentOS 6.5

Hi, That looks weird. Can you compile a sample OpenMP code, e.g. this https://computing.llnl.gov/tutorials/openMP/samples/C/omp_hello.c -- Szilárd On Fri, Jul 7, 2017 at 11:59 AM, Seyed Mostafa Razavi wrote: > Hello, > > I'm trying to install Gromacs (gromacs-2016.3) on

Re: [gmx-users] about quality of CPUs with GPUS

Hi, By quality are you referring to performance? The ideal CPU-GPU balance depends on the type of runs (system, settings, FF) too. However, in most cases, for current GROMACS versions you will need many and fast cores to balance with the 1080 Ti -- which is about the fastest gaming GPU out there.

[gmx-users] about quality of CPUs with GPUS

Dear all, Normally with 2GPU, 8CPUs or 16 CPUs are used for a system for better performance. Do you have any idea whether gromacs performance depends on the quality of these CPUs? if does so then how much differ for E5 2640 v4 and E5 2667 v4. And for ES5 2667 v4 and ES5 2680 v4. We are

Re: [gmx-users] problem: gromacs run on gpu

Hi, you can try using ntmpi XX ntomp XXX and try to use the combinations for more details. http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html. Further, I think it's better to use 2 x Tesla K40 instead of using all three. You may see a performance reduction due to load

[gmx-users] TIP3P WATER

I have recently started using gromacs and would appreciate if someone could guide me how to create a tip3p water droplet. -- 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

[gmx-users] problem: gromacs run on gpu

Dear Gromacs users, I installed Gromacs 5.1.3. on GPU in Rocks cluster system. After using command: gmx_mpi mdrun -nb gpu -v -deffnm old_gpu, I encountered with: = GROMACS: gmx mdrun, VERSION 5.1.3 Executable:

[gmx-users] Equilibration

blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } HiI am a new GROMACS user and i am trying to run a simulation on 4LY1 protein and my designed drug to check their

[gmx-users] Gromacs installation fails in CentOS 6.5

Hello, I'm trying to install Gromacs (gromacs-2016.3) on my CentOS 6.5 system. I exactly follow the installation instruction in http://manual.gromacs.org/ documentation/2016.3/install-guide/index.html. After I run "make", the installation process starts and proceeds to %97, then it gives me an

Re: [gmx-users] protein protein interaction: side chain contribution

Hi Justin, Thanks a lot for the advice. It looks like I had put one atom in the wrong index group. After correction my results looks as follows: Energy Average Err.Est. RMSD Tot-Drift ---

Re: [gmx-users] gmx wham problem

do you have any suggestions??? thanks Emiliano On 2017-07-01 14:01, edesantis wrote: Dear Matthew, thanks for your opinion. How can you establish if the histograms are sufficiently overlapped? Is there any thumbs role? For what concern the negative sign of reaction coordinates, I think it