Re: [gmx-users] question about applying surface tension

Dear Justin thanks for your answer actually I'm trying to reproduce other constant surface tension simulations of bilayers to make sure my method is right. they calculate area per lipid for different surface tensions from approximately 0 to 100 dyn/cm and that is why I've mdp files with different

Re: [gmx-users] Using the md integrator for calculating free energy of solvation

I ran equilibrium simulations, and then a longer simulations with the recommended sd integrator. Still, the mass_lambda dH/dL is nonzero and sometimes it is the dominant contribution at certain lambdas. I don't think it is a convergence issue because there aren't huge fluctuations in dH/dL values

Re: [gmx-users] question about applying surface tension

On 5/12/17 12:27 PM, Ali Shomali wrote: Dear Justin Is there any possibility that the cause of problem is my simulation time ? (3 ns) Yes, that's about 50 times too short to be credible. Lipids relax over tens of nanoseconds, and typical production run times for well equilibrated membrane

Re: [gmx-users] question about applying surface tension

Dear Justin Is there any possibility that the cause of problem is my simulation time ? (3 ns) On Mon, May 8, 2017 at 4:38 PM, Justin Lemkul wrote: > > > On 5/7/17 2:56 PM, Ali Shomali wrote: > >> Thanks so much Justin for your answer. actually I performed different >>

Re: [gmx-users] question about applying surface tension

Dear Justin thanks for the answer I think the surface tension line was deleted in email by mistake , sorry for that. I managed to perform other simulations for DMPC and DPPC . in all of them I applied reported surface tensions ( twice the reported surface tension per interface) in all of them my

Re: [gmx-users] NVML does not come separate starting from Cuda 8.0

Hi, There already is an applicable Redmine ( https://redmine.gromacs.org/issues/2061). Ake's observations agreed with two CUDA 8.0 installs I checked, so it looks like CUDA 8.0 acquired the header and stub library, but the driver package still has the real library. We can't really / shouldn't try

Re: [gmx-users] RMSF problem

Also, knowing the group you selected in the mdp for writing the xtc file is key to understanding why what you get might not match what you are trying to do... Mark On Fri, May 12, 2017 at 1:51 PM Justin Lemkul wrote: > > > On 5/11/17 1:43 PM, Franco Henrique wrote: > > Dear

Re: [gmx-users] RMSF problem

On 5/11/17 1:43 PM, Franco Henrique wrote: Dear Justin Lemkul, Thank’s for prompt reply. My protein has 198 aminoacides (PDB: 2GOJ; http://www.rcsb.org/pdb/explore.do?structureId=2GOJ). After RMSF command (gmx rmsf -f .xtc -s .tpr -o .xvg -res), the output has only 103 aminoacides as

Re: [gmx-users] NVML does not come separate starting from Cuda 8.0

CUDA 8.0.61_375_26 does not contain the actual NVML lib, only stubs. And NVML is still separate from the CUDA package as far as i can see. The libnvidia-ml.so in /lib64/stubs is much smaller than the actual library. On 05/12/2017 01:11 PM, Szilárd Páll wrote: > Mat, > > Thanks for the report. I

Re: [gmx-users] NVML does not come separate starting from Cuda 8.0

Mat, Thanks for the report. I was under the impression that this should have "just worked" given that NVML is now in the toolkit, but if it does not, we should look into it. Can you please, file an issue on redmine.gromacs.org (with reproducing steps). Cheers, -- Szilárd On Fri, May 12, 2017

[gmx-users] NVML does not come separate starting from Cuda 8.0

CUDA starting from the version 8.0 is not separated from the NVML library any more, and cannot be downloaded independently. NVML is part of the toolkit. However, the documentation requires the GPU_DEPLOYMENT_KIT_ROOT_DIR to find NVML. I have tried setting the variable to multiple combinations

Re: [gmx-users] New residue for custom capping

Mark, Thanks Mark! Indeed it was the problem. I forgot to update residuetypes.dat. Regards, Simon 2017-05-12 15:46 GMT+08:00 Mark Abraham : > Hi, > > Those define your residue, but do not classify it, so pdb2gmx doesn't know > that protein-specific termini are

Re: [gmx-users] New residue for custom capping

Hi, Those define your residue, but do not classify it, so pdb2gmx doesn't know that protein-specific termini are appropriate. >From the link I provided: "Add your residue to residuetypes.dat with the appropriate specification (Protein, DNA, Ion, etc)." Mark On Fri, May 12, 2017 at 9:39 AM

Re: [gmx-users] New residue for custom capping

Dear Mark, Thanks for your prompt reply. I have already updated my .rtp and .hdb for my new residue. Would you mind to suggest which file I am missing? I am happy to provide relevant parts of .rtp and .hdb if necessary. Regards, Simon 2017-05-12 15:31 GMT+08:00 Mark Abraham

Re: [gmx-users] New residue for custom capping

Hi, I suspect you need to add your residue to the class of Protein residues, per http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field Mark On Fri, May 12, 2017 at 9:05 AM Simon Kit Sang Chu wrote: > Hi everyone, > > I am using a new forcefield

[gmx-users] New residue for custom capping

Hi everyone, I am using a new forcefield which does not give proper neutral capping, but requires me to create a custom made residue for that purpose. Specifically, I want a NH2 cap instead of NH+. I rename VAL1 into VAT1, update .hdb & .rtp. However, when I pdb2gmx -ter to create a topology