[gmx-users] simulating multiple objects in the same box
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 chain topologies
; Include water topology
; Include generic ion topology
[ system ]
Two proteins in water
[ molecules ]
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.
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