[gmx-users] Atom definition in atomname2type.n2t file

Hi, I like to use x2top command to generate a primitive topology file for Graphene Oxide, where I have defined new Atoms with new Types. This requires a file, *atomname2type.n2t *that contains data like this, Copls_157-0.18 12.011 4H 0.108 H 0.108 H 0.108 C 0.150 Copls_158

Re: [gmx-users] Conversion Amber to Gromacs

ParmEd (https://parmed.github.io/ParmEd/html/parmed.html) would be the appropriate software for converting topologies. This is the parm.py script I have employed, supply amber topologies file.prmtop and file.inpcrd as input and amber.save option will give converted gromacs topologies as output. i

Re: [gmx-users] Conversion Amber to Gromacs

You can do with ParmEd On Oct 20, 2017 10:07 PM, "Elisa Pieri" wrote: > Hello GMX users/developers, > > we are trying to add the Amber lipids17 forcefield to the Amber99 > forcefield implemented in Gromacs. We are a little bit lost on the torsion > parameters: how to convert the constant from Amb

[gmx-users] Conversion Amber to Gromacs

Hello GMX users/developers, we are trying to add the Amber lipids17 forcefield to the Amber99 forcefield implemented in Gromacs. We are a little bit lost on the torsion parameters: how to convert the constant from Amber to Gromacs? Thank you in advance! Elisa -- Gromacs Users mailing list * Ple

Re: [gmx-users] Fwd: What is the meaning of max(|Fn|) in the Energy Minimization?

Hi, max(|Fn|) is the scalar force on an atom that is the largest of the scalar force on each atom at that step. The subscript n refers to the step number. I have fixed the documentation at https://gerrit.gromacs.org/#/c/7058/, because "component" was not the best choice of word. Mark On Fri, Oct

[gmx-users] Fwd: What is the meaning of max(|Fn|) in the Energy Minimization?

Hi all, I have a question about the definition of the maximum force during the energy minimization. >From the Gromacs Manual 2016.4 -- 3.10.1 Steepest Descent -- The notation max(|Fn|) means the largest of the absolute values of the force components. Does this mean that (1) for a specific atoms

Re: [gmx-users] Energy Minimization Error

Dear Gromacs users, When I tried to run the equilibration run, it gave several LINCS WARNINGS. However, that equilibration run is completed by the Gromacs. Do I have to concern about these warnings or can I ignore those? Thank you. Sincerely, A. Guruge On Fri, Oct 20, 2017 at 11:22 AM, Justin L

[gmx-users] non-zero total charge

Hi, I am simulating one component system (tabulated potential), and they have similar charge. So the total charge of the system is non-zero. The program properly works. Should I still worry? Thanks for answer Best regards -- Gromacs Users mailing list * Please search the archive at http://www.