Re: [gmx-users] Optimising mdrun

Hi - > This setting is using 16 MPI process and using 2 OpenMP thrads per MPI proces With ntomp 1 you should only be getting one OpenMP thread, not sure why that's not working. Can you post a link to a log file? For a small system like that and a powerful GPU, you're likely going to have some

Re: [gmx-users] PCA analysis with different atoms in -s and -f

Dear Zhang Chen, In order to calculate the covariance matrix, you have to decide what will be the reference frame. I suggest play around with option "-ref no/yes". The reference can be the average coordinates of the C-alpha atoms of the protein of trajectory 0.pdb. Now, if you changed only the

[gmx-users] converting gromacs topology file to namd topology file

Hello Dear Gromacs users, I hope this email finds you well. I am sending this email to ask is there any way I can convert gromacs topology file (.itp) to namd (top) file? I appreciate any help, Best regards, Hadi -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Onsager coefficient

Dear Mr Spoel, I have found out that I couldn't attach an image and I am sorry about that. here is a link to the picture. https://cdn1.imggmi.com/uploads/2020/4/1/1599cd9ac1102e329ff91759d3314725-full.png On Tue, 31 Mar 2020 at 09:59, David van der Spoel wrote: > Den 2020-03-30 kl. 22:51, skrev

[gmx-users] Reviewing docking resluts

Hi everyone This may be irrelevant to the list but i have a big problem. I have designed some inhibitors using molecular docking and then performed 10 nsmd simulations. I have to submit the article for publication. But the journal is asking for the names of persons to review the article. Can you

Re: [gmx-users] Problem with REST2

Okay, now I understand what you mean. Then I should try deleting the underscores in the created top files. This really startled me though, because I never had this problem in the past. Thanks for your help! Best, Benjamin > Am 01.04.2020 um 20:20 schrieb Daniel Burns : > > Once you run your

Re: [gmx-users] Problem with REST2

Once you run your processed.top with selected hot atoms (via underscore) through the plumed script, the new .top files (denoted with numbers) should have scaled values replaced in the appropriate places. Compare the charges for instance on the selected atoms in your original processed.top and the

Re: [gmx-users] Problem with REST2

Dear Daniel, I thought the underscores in the processed.gro file are necessary in order to mark the hot atoms and am not sure if all atoms are recognised as cold atoms when deleting the underscores. Best, Benjamin > Am 01.04.2020 um 19:10 schrieb Daniel Burns : > > I haven't had an error

Re: [gmx-users] Problem with REST2

I haven't had an error from the underscore myself but I haven't been using the Amber force field. Maybe you could try deleting the underscores on the input .top files since the plumed script has already scaled them. The atomtype might be recognized then. On Wed, Apr 1, 2020 at 11:25 AM Joseph,

[gmx-users] Free energy of protonation

Dear list, I am trying to calculate the free energy for protonating a single monomer of oleic acid with the martini forcefield. This in preparation for other work, and I wanted to start by reproducing what is already done. To do this, I have defined the following in my topology to describe the

[gmx-users] Problem with REST2

Dear members of the gromacs mailing list, I have problems setting up REST2 (replica exchange with solute tempering) calculations. The version of PLUMED with GROMACS I use is GROMACS/2018.3-plumed and the forcefield I am using is amber14sb_parmbsc1.ff. The error occurs when I try to set up the

Re: [gmx-users] 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out

On 4/1/20 12:04 AM, Seketoulie Keretsu wrote: Dear Gromacs Community, I have come across this problem during NVT equilibration of an all atom protein-ligand MD simulation. Fatal error: 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out of the domain decomposition

Re: [gmx-users] 1-4 LJ interactions

On 4/1/20 8:57 AM, Andrey Gurtovenko wrote: Dear Justin, thank you for the clarification. I think my confusion is in part due to the urea topology file used in the manual as an example, which does not contain the [pairs] section. Urea is probably a poor example because it actually doesn't

Re: [gmx-users] 1-4 LJ interactions

Dear Justin, thank you for the clarification. I think my confusion is in part due to the urea topology file used in the manual as an example, which does not contain the [pairs] section. with kind regards, Andrey On Wed, Apr 1, 2020 at 3:32 AM Justin Lemkul wrote: > > > > On 3/31/20 12:59 PM,

[gmx-users] GROMACS mailing-list will move to a forum

Hello gmx-users! We have been working behind the scenes the last few months on some changes to the organization of the GROMACS project, one of them is switching our gmx-users mailing list to a forum We are continuously re-thinking about how we can best engage with you and how people can get

Re: [gmx-users] Optimising mdrun

Hi, I'm trying to use GROMACS 2019.3 on two different machines, simulating the same system. The system is made up of 100 identical molecules, consisting of 61 united atoms each, in a non-aqueous system. I am however getting vastly different performance on the two machines, and I don't really