Re: [gmx-users] strange GPU load distribution

Hi Szilárd, It really does appear that GMX_DISABLE_GPU_DETECTION=1 in the user's .bashrc fixed it right up. We haven't tried his runs alongside GPU-accelerated jobs yet, but he reports that none of his PIDs ever appear in nvidia-smi anymore and overall his jobs start much faster. This was an

Re: [gmx-users] Secondary structure of peptides

On 5/7/18 10:57 PM, m g wrote: Dera Justin,I tried to obtained .eps file for my peptides with this command "gmx xpm2ps -f ss.xpm -o ss.eps -bx 1 -by 30", but unfortunately I can't obtained a good .eps file that show me the secondary structure.  I tried another value for -bx and -by  flags,

[gmx-users] table_A_B

Dear all, I have two non-boded parameters of C6 and C12 for the interaction between two atoms of A and B. Would you please give me a script to generate table_A_B.xvg out of those parameters? Thank you. Alex -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Proper ensemble for lateral diffusion coefficient

Hello Everyone, I am running simmulations in order to study the lateral diffusion coefficient of small molecules (eg. pyrene carboxylic acid) adsorbed at liquid interfaces. The system is made of a liquid phase in contact with various organic solvents, and tens of molecules are adsorbed at the

Re: [gmx-users] pure methane condensation in NVT simulation

It isn't possible for two identical setups to produce two different results. That is, if they are actually identical, i.e. what Justin asked earlier. You are only sharing a small portion of your input. It also isn't clear what "normal box" and "the result will be correct as we think" mean,

Re: [gmx-users] pure methane condensation in NVT simulation

On 5/8/18 10:11 AM, 耿明 wrote: I tried my simulation with another MD code package using the same potential model and initial configuration. And the result is correct, I get a homogenous gas phase of methane. I have checked my settings in Gromacs several times, But still do not find where

Re: [gmx-users] KCl forms crystals at c=0.15M with amber99sb-ildn

Hi, I think the problem comes from the ion parameters within the "vanilla" amber forcefieCld. If I'm not mistaken, the parameters in the gromacs port are the Aqvist parameters, which are known to make this little trick. In the past, we have used the Smith/Dang parameters for simulations

Re: [gmx-users] gromacs 2018 make error with multiple compilers and GPU support

> Yes CentOS 6 would be worse in the same way that using a horse would be > worse than driving a Model T in 2018. :-) I totally agree, but unfortunately my home cluster still uses RHEL 6.7 and another cluster we have an allocation for uses Centos 6.7. ¯\_(ツ)_/¯ Thanks for the help! On Tue, May

Re: [gmx-users] pure methane condensation in NVT simulation

I tried my simulation with another MD code package using the same potential model and initial configuration. And the result is correct, I get a homogenous gas phase of methane. I have checked my settings in Gromacs several times, But still do not find where could be wrong. Can anyone share me a

[gmx-users] KCl forms crystals at c=0.15M with amber99sb-ildn

Hello, We are trying to use amber99sb-ildn with gromacs2018.1 for simulations of a protein in a salt solution. However, we observed that KCl seems to form stable salt crystals even at concentrations as low as 0.15 mol/l at T=298K in our system. Our MDP options have been taken from

Re: [gmx-users] gromacs 2018 make error with multiple compilers and GPU support

On Tue, May 8, 2018 at 3:54 PM Kevin Boyd wrote: > Thanks for the reply. > > The distro is actually relatively up to date, from what I can tell gcc > 4.8.5 is all that CUDA supports for the most recent versions of RHEL > and Centos. CUDA is just supporting the stock

Re: [gmx-users] replicates with different random seed

If you use the .cpt file then the velocities will be provided as from the checkpoint. This would effectually only lengthen the simulation. In order to truly sample the simulation space from a "random" seed, you should reassign velocities from scratch as in the .mdp file. In *principle* the

Re: [gmx-users] Contraints on both angles and dihedrals

Hi, There is no general support for rigid body dynamics in GROMACS. Mark On Tue, May 8, 2018, 12:52 Qasim Pars wrote: > Dear users, > > I would like to constraint all the angles and dihedrals of a ligand to > make it rigid but Gromacs does not have this capability for the

[gmx-users] Contraints on both angles and dihedrals

Dear users, I would like to constraint all the angles and dihedrals of a ligand to make it rigid but Gromacs does not have this capability for the dihedrals. However, the angle and dihedral restraints do not make it rigid as I want, as it is very flexible. Do you have an idea on how I can

Re: [gmx-users] pure methane condensation in NVT simulation

On 5/8/18 6:34 AM, Ming Geng wrote: Thanks Alex, "common NVT" I mean is the simulation is only using the T coupling and no P coupling. The T P coupling part was set as following *;; TEMPERATURE COUPLING* * ; Temperature coupling methods * * Tcoupl =

Re: [gmx-users] pure methane condensation in NVT simulation

Thanks Alex, "common NVT" I mean is the simulation is only using the T coupling and no P coupling. The T P coupling part was set as following *;; TEMPERATURE COUPLING* * ; Temperature coupling methods * * Tcoupl = nose-hoover* * ; frequency for coupling

Re: [gmx-users] pure methane condensation in NVT simulation

"Common NVT" and not properly set up NPT for organic fluid simulations? What could possibly go wrong... Alex On May 8, 2018 3:15 AM, "Ming Geng" wrote: Dear all, We are trying some MD simulations with Gromacs recently. And we found some weird phenomenon in

[gmx-users] pure methane condensation in NVT simulation

Dear all, We are trying some MD simulations with Gromacs recently. And we found some weird phenomenon in our test. We have about 20k pure methane in a long box(4 x 4 x 180 nm). We use OPLS-UA for methane molecule. After a 70ns of common NVT simulation, we found the methane begin to

Re: [gmx-users] replicates with different random seed

Ideally, you should repeat your entire procedure with a new seed from the step that first generates velocities. Repeating hundreds of nanoseconds of simulation a few times probably would not be my response to your likely 85 year old reviewer, but I hope this helps. Alex On May 8, 2018 2:58 AM,

[gmx-users] replicates with different random seed

Hello all, I have submitted a paper with 100ns simulations data, however reviewer suggested to provide replicates with different random seeds. I have used below lines in the mdp file of equilibration step for my first simulation. now i am confused for replicates (minimum 2) whether i have to