[gmx-users] Segfaults when using Replica Exchange

I'm having an issue where GROMACS is generating segfaults when I try to run replica exchange simulations on a system of ~300,000 atoms using 20 temperature points and around 10,000 cores. This happens when using either the 2016.3 version or the 5.1.2 version of the code, and I've tried vary

Re: [gmx-users] GMX 2018 regression tests: cufftPlanMany R2C plan failure (error code 5)

And this is with: > gcc --version > gcc (Ubuntu 5.4.0-6ubuntu1~16.04.6) 5.4.0 20160609 On Tue, Feb 6, 2018 at 1:18 PM, Alex wrote: > Hi all, > > I've just built the latest version and regression tests are running. Here > is one error: > > "Program: mdrun-test, version 2018 > Source file: s

[gmx-users] GMX 2018 regression tests: cufftPlanMany R2C plan failure (error code 5)

Hi all, I've just built the latest version and regression tests are running. Here is one error: "Program: mdrun-test, version 2018 Source file: src/gromacs/ewald/pme-3dfft.cu (line 56) Fatal error: cufftPlanMany R2C plan failure (error code 5)" This is with CUDA 9.1. Anything to worry abou

Re: [gmx-users] pdb2gmx "dangling bond" error when trying to make periodically connected DNA

Hi again, It seems from previous posts that this type of system setup is of general interest so I thought I'd share the solution(s). I modified the tdb file for the 5' end, here for CHARMM27, by adding the following to the end of dna.n.tdb [ hack ] [ replace ] C5' C5' CN8B12.011

[gmx-users] PCA mathematical information

Dear gromacs users, I am a PhD student in biophysics, I am trying to preform principal component analysis on my simulations with the aim to understand if there are present correlated motions during the dynamics. I an not expert of this kind of analysis, I was studying different tutorials and

[gmx-users] trjcat accepts only binary formats

Dear Gromacs Developers, I have found that in version 2018 the trjcat program stopped supporting .gro as an input file for the switch "-f". I have been using this feature to concatenate several coordinate states to calculate single point energy with gmx mdrun -rerun. I have found a workaround to

Re: [gmx-users] gmx hbond

Hi Negar, Correct, the -dist option doesn’t do what you want it to. I cannot come up with a recipe for how to do this, but I suspect multiple rounds of gmx select and gmx hbond might do the trick. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodo

[gmx-users] Gibbs' free energy in MD

Hi! How can I calculate Gibbs' free energy from the potential energy values obtained from the MD simulation? Regards, Raag -- 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 http://www.gro

Re: [gmx-users] Rupture force definition

Thank you very much Justin. Here it is working but having some problem. pull_group2_name = chain_B35 is moving in the + z direction & pull_group4_name= chain_B26 is moving oppositely in the -z direction While I have given pull in +z direction for both the above group. Note - pull_group1_name