Iskinder Arsano

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Questions related from Iskinder Arsano

How can I avoid intramolecular RDF peaks in Gromacs?

The Gromacs manual has the following regarding exclusions: "If a run input file is supplied (-s) and -rdf is set to atom, exclusions defined in that file are taken into account when calculating...

27 July 2021 1,633 1 View

Anyone use GROMACS' pdb2gmx for Adenosine monophosphate (AMP) to use with CHARMM force field?

I am trying to use the following command in GROMACS to generate a CHARMM topology file: gmx pdb2gmx -ff charmm27 -f amp.pdb -o amp.gro -p amp.top The atom list in my pdb file (amp.pdb)...

02 February 2021 7,966 6 View

GROMACS: how do I know how many box images a particular atom has moved from from t=0 to t=N?

In GROMACS how do I know how many box images a particular atom has moved from from t=0 to t=N? LAMMPS, for example, has the option to include image flags in the dump file for x, y, and z. Is there...

31 January 2021 9,039 3 View