[gmx-users] multiple molecules of same type and .top file

Chetan Mahajan chetanvm10 at gmail.com
Mon May 12 08:43:10 CEST 2014

Dear All,

I am trying to generate .top file for my system. I would be obliged if you
could explain following topology file question to me, since it is not very
clearly mentioned anywhere:

In LAMMPS software that I am used to, user is required to enter details of
topology for all the molecules of same type e.g. if there are 1000 formate
ions, one needs to enter atoms, bonds, angles, dihedrals for all 1000
formate ions. Is this the case for GROMACS or only one representational
topology for 1 molecule of that type is sufficient? Atoms section in .top
file in gromacs does contain column for residue number (resi or resnr) in a
given [moleculetype], so I would guess probably I need to enter all the
molecules of a given type, although it is not the case for water?

Thanks a lot!


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