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

[Justin Lemkul]

On 7/22/14, 2:33 AM, 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.
>
> Thanks in advance.
>

Please see my reply from yesterday to this same question:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-July/090834.html

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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