[gmx-users] Per atom energies

Hi all, I look on google for any answers for such question in this maillist, and I found related questions but no final answer. I wish to compute the heat flux for my system using GK relations. I found the gromacs extension force the calculation of the per atom stress

Re: [gmx-users] Lincs warning in free energy calculation

Check the forcefield you are using is appropriate for your system or there might be some problem with the ligand parameters. On Tue, Mar 24, 2020 at 11:30 AM Sadaf Rani wrote: > Dear Gromacs users > I ran an MD simulation for 3ns and from the last coordinates started a free > energy

[gmx-users] no atom pairs for dispersion correction

Dear Gromacs users I am running an MD simulation of the protein-ligand complex. At the start of the production run, I am getting this warning. What does it mean and how should I fix it? *WARNING: There are no atom pairs for dispersion correction* Thanks in advance. Sadaf -- Gromacs Users

Re: [gmx-users] Parrinello-Rahman and Pairtype1 causing pressure instabilities

Hey y'all, Ran some additional simulations and, unfortunately, I'm still experiencing problems. Here's the mdp file that I used: integrator = md nsteps = 2000 ; 20 ns dt = 0.001000 nstlist = 20 ns_type =

[gmx-users] Water molecules fill in gaps in protein

Dear Gromacs Users, I noticed that quite often after adding the solvent (water) to the protein, the water molecules fill in gaps inside the protein which are not occupied. I am afraid that since their position may not be optimal (they actually should not be there), it will lead to artifacts as

Re: [gmx-users] SARS-CoV-2 main protease with ligand from acpype, but converting to vsites?

Hi Bjorn, This is still the recommended procedure. Contact me directly if you need help with the conversion to an rtp file.Best, Christian Original message From: Bjorn Wesen Date: 27/03/2020 17:16 (GMT+01:00) To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users]

Re: [gmx-users] SARS-CoV-2 main protease with ligand from acpype, but converting to vsites?

Hi Bjorn, This is still the recommended procedure. Contact me directly if you need help with the conversion to an rtp file.Best, Christian Original message From: Bjorn Wesen Date: 27/03/2020 17:16 (GMT+01:00) To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users]

[gmx-users] Multi-GPU optimization, "DD without halo exchange is not supported"

Dear users, I'm trying to optimize the execution of a system composed by 10 million atoms on a multi-GPU machine with GROMACS 2020.1. I've followed the instructions given at https://devblogs.nvidia.com/creating-faster-molecular-dynamics-simulations-with-gromacs-2020/ . However, when I

Re: [gmx-users] compile with intel compiler

Hi, I use the following combination with Intel PSXE. It works and your problem is likely related to the name of the Intel CXX compiler. source /opt/intel/compilers_and_libraries/linux/bin/compilervars.sh intel64 source /opt/intel/impi/2018.4.274/bin64/mpivars.sh source

[gmx-users] SARS-CoV-2 main protease with ligand from acpype, but converting to vsites?

Hi list, I have a working sim of the solvated SARS-CoV-2 main protease dimer from https://www.rcsb.org/structure/6Y84 using amber99sb-ildn and pdb2gmx-generated vsites for speed, and wanted to proceed by adding some of the various proposed inhibitor ligands to the sim for further workflow

Re: [gmx-users] unexpecter rmsd

Thank you Justin On Fri, Mar 27, 2020, 19:47 Justin Lemkul wrote: > > > On 3/27/20 11:10 AM, Emran Heshmati wrote: > > Thanks to Paul and jorden, I repost my question: > > I am working on a protein consisting 2 chains. After performing > > regular MD simulation > > and analysis the outputs, I

Re: [gmx-users] unexpecter rmsd

On 3/27/20 11:10 AM, Emran Heshmati wrote: Thanks to Paul and jorden, I repost my question: I am working on a protein consisting 2 chains. After performing regular MD simulation and analysis the outputs, I got unexpecter rmsd, as seen in link below. What is the problem??

[gmx-users] unexpecter rmsd

Thanks to Paul and jorden, I repost my question: I am working on a protein consisting 2 chains. After performing regular MD simulation and analysis the outputs, I got unexpecter rmsd, as seen in link below. What is the problem??

Re: [gmx-users] Inexpected rmsd

Hello, you can't attach files here on the mailing list. Please upload the file somewhere and share a link to it. Cheers Paul On 27/03/2020 10:35, Jorden Cabal wrote: Dear Emran Heshmati, I can not see any graph? Did you attach it. Please verify. Thank you On Fri, Mar 27, 2020 at 6:21 PM

Re: [gmx-users] Inexpected rmsd

Dear Emran Heshmati, I can not see any graph? Did you attach it. Please verify. Thank you On Fri, Mar 27, 2020 at 6:21 PM Emran Heshmati wrote: > I am working on a protein consisting 2 chains. After performing regular MD > simulation and analysis the outputs, I got unexpecter rmsd, as shown in

[gmx-users] Inexpected rmsd

I am working on a protein consisting 2 chains. After performing regular MD simulation and analysis the outputs, I got unexpecter rmsd, as shown in arttached graph. What is the problem? -- Gromacs Users mailing list * Please search the archive at