Re: CONVERT PSF to TOP grimaces

From: Vermaas, Josh (
Date: Sun Oct 31 2021 - 15:02:48 CDT

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: <> on behalf of "ROPÓN-PALACIOS G." <>
Reply-To: "" <>, ""ROPÓN-PALACIOS G."" <>
Date: Sunday, October 31, 2021 at 3:19 PM
To: "" <>
Subject: namd-l: CONVERT PSF to TOP grimaces

Dear Users,

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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