[gmx-users] simulating multiple objects in the same box

ibrahim khalil ibrahim.khalil.chem at gmail.com
Tue Jul 22 08:33:30 CEST 2014

Hi I am new to gromacs. I am trying to simulate 2 different objects in the
same box. The two objects are CNT and a biomolecule. For the CNT i am using
a slightly modified forcefield from the oplsaa and for the bio molecule i
am using the oplsaa force field.

I am stuck at building the topology file. i saw the tutorial of simulating
multiple proteins in the same box but in my case i have 2 different
forcefields. My topology file is -

#include "./cnt_oplsaa.ff/forcefield.itp"

; Include chain topologies
#include "cnt1.itp"
#include "k.itp"

; Include water topology
#include "spce.itp"

; Include generic ion topology
#include "ions.itp"

[ system ]
Two proteins in water

[ molecules ]
CNT        1
Protein     1

But whenever I run grompp i get errors like -

Atoms in the .top are not numbered consecutively from 1 (rather, atomnr =
1, while at->nr = 3)

It would be very nice if someone could help me with the steps to prepare
the .top file.

Thanks in advance.

More information about the gromacs.org_gmx-users mailing list