[gmx-users] Topology regarding

RAHUL SURESH drrahulsuresh at gmail.com
Fri May 10 17:25:51 CEST 2019

Hi gromacs users.

To simulate a non-protein, (definitely not a small molecule), a molecule
with 200 atoms, composing of C, N and H only, any suggestions to start with
the groundwork?
Precisely, if I am starting with updating the ff, ie to update the rtp
entry for the molecule in atomtypes.rtp, is it compulsory to name the
repeating atoms with different names?
Can i name all the carbon to be C and Nitrogen to be N and Hydrogen to be H?

Should I also update bonded and nonbonded files and hdb files?

I kindly request your valuable suggestions. Please.

*Rahul *

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