Re: [gmx-users] Bilayer exploding with semiisotropic coupling

Hello, please upload the log file from the run, as well as the command you used to run the simulation and your system specs (processor, whether you are using GPUs). Then we can see what is wrong here. Thanks in advance. Cheers Paul On Sat, 4 Jan 2020, 21:14 Kevin Boyd, wrote: > Hi, > > Can

Re: [gmx-users] Bilayer exploding with semiisotropic coupling

Hi, Can you share more information? Please upload your starting configuration and a log file. On Fri, Jan 3, 2020 at 10:29 AM Namit Chaudhary wrote: > Hi, > > Sorry. I didn't realize that attachments aren't uploaded. Below is a link > for the files mentioned in the original mail. > >

Re: [gmx-users] Gromacs 2019 - Ryzen Architecture

Hi, A few things besides any Ryzen-specific issues. First, your pinoffset for the second one should be 16, not 17. The way yours is set up, you're running on cores 0-15, then Gromacs will detect that your second simulation parameters are invalid (because from cores 17-32, core 32 does not exist)

Re: [gmx-users] GROMOS forcefields

Thank you for such a detailed response. The explanation was very helpful. On Sat, Jan 4, 2020 at 10:00 PM Kenny Goossens wrote: > Hi Shakkira, > > In each of the consecutice iterations of the GROMOS force field, a > reparameterization of the constants was performed in order to reproduce >

Re: [gmx-users] [gmx-user] Autodock Vina Out use in gromacs MD

Dear Proffesor Lemkul, I have given below the MD RMSD for complex, and noted that Ligand is getting detached again. When I viewed the trajectory on VMD it was confirmed. The ligand did not abruptly got dislodged instead it slowly came out of binding pocket and started moving around after.

Re: [gmx-users] GROMACS 2020 official release

Hello again, I got notified that there is an issue for the first link, it needs to be without the final dot: http://manual.gromacs.org/2020/release-notes/index.html Sorry for the inconvenience and happy new year! Cheers Paul On 01/01/2020 18:11, Paul bauer wrote: Hello GROMACS users!

Re: [gmx-users] query regarding center of mass removal

On 1/4/20 1:38 AM, Snehasis Chatterjee wrote: Thank you Prof. Lemkul for your kind reply. In mdp file, I will set comm_grps to "system". But in tc-grps, can I couple capsid with Ca2+ ions? 240 Ca2+ ions are non-covalently attached with the capsid and have important role in maintaining capsid

Re: [gmx-users] GROMOS forcefields

Very informative and interesting. I was using 54a7 forcefield with GROMACS 2018.4. I was confused with mdp parameters. Which version of GROMACS should I use if I want to employ 54a7 force field? On Sat, 4 Jan 2020, 22:00 Kenny Goossens, wrote: > Hi Shakkira, > > In each of the consecutice

Re: [gmx-users] GROMOS forcefields

On 1/4/20 11:29 AM, Kenny Goossens wrote: Hi Shakkira, In each of the consecutice iterations of the GROMOS force field, a reparameterization of the constants was performed in order to reproduce experimental data for various molecules (in the case of the GROMOS suite, parameterization is

Re: [gmx-users] GROMOS forcefields

Hi Shakkira, In each of the consecutice iterations of the GROMOS force field, a reparameterization of the constants was performed in order to reproduce experimental data for various molecules (in the case of the GROMOS suite, parameterization is mainly fitted to free enthalpy of solvation).

[gmx-users] GROMOS forcefields

Hi all Can anyone explain the different code seen in forcefields of GROMOS like 53A6, 54A7, 43a1,. what does these numbers mean? -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 -- Gromacs Users mailing list * Please

[gmx-users] The pull code

Dear gromacs users, I am tryingto make a shear flow in an electrolyte by moving two parallel bilayers immersedin the electrolyte in opposite directions. I use the following pull code (wherethe groups low and up are the two moving bilayers): pull = yespull-coord1-type =