[gmx-users] simulating multiple objects in the same box
jalemkul at vt.edu
Tue Jul 22 01:20:07 CEST 2014
On 7/21/14, 4:40 PM, ibrahim khalil wrote:
> 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.
Every [moleculetype] must be numbered consecutively from 1, as the error states.
You have a [moleculetype] for which that is not true. Identify it, and
re-create the topology correctly.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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