From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Sun Oct 31 2021 - 15:53:27 CDT
The list of parameters you’d pass to TopoGromacs is the same list you’d pass to NAMD, since you need to be able to match a parameter to every term in the simulation system. TopoGromacs won’t enforce the matching, since it assumes you know what you are doing, but if you make a mistake grompp will tell you about missing parameters.
From: "ROPÓN-PALACIOS G." <biodano.geo_at_gmail.com>
Date: Sunday, October 31, 2021 at 4:12 PM
To: "Vermaas, Josh" <vermaasj_at_msu.edu>
Subject: Re: namd-l: CONVERT PSF to TOP grimaces
Dear Josh, thank you very much, for your prompt reply. Well I assume that the preparation of the system in PSFgen is all "ok", I could use multiple parameters in the list of topoGromacs parameters, which do not necessarily represent the molecular of my system, if not some more that can help to not have missing parameters for any particular atom?
On Oct 31, 2021, at 15:02, Vermaas, Josh <vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu>> wrote:
I might be a little biased since I wrote TopoGromacs for my own needs, but I think it’s a fine way to generate the .top file GROMACS expects. This defines the system topology and parameters, which are combined with a .mdp file into the .tpr files mdrun uses to conduct simulations.
From: <owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>> on behalf of "ROPÓN-PALACIOS G." <biodano.geo_at_gmail.com<mailto:biodano.geo_at_gmail.com>>
Reply-To: "namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>" <namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>>, ""ROPÓN-PALACIOS G."" <biodano.geo_at_gmail.com<mailto:biodano.geo_at_gmail.com>>
Date: Sunday, October 31, 2021 at 3:19 PM
To: "namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>" <namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>>
Subject: namd-l: CONVERT PSF to TOP grimaces
Based in rigid characteristics of gromacs (pdb2gmx) for manipule and build complex system, I’ve used PSFgen embebed into VMD to build my system. Now I like convert PSF to Top gromacs, using TopoGromacs tool.
My question is: It is right pathway to perform md simulations with gromacs?
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