[gmx-developers] bonding problem in simulating multiple objects in the same box

Justin Lemkul jalemkul at vt.edu
Tue Feb 4 19:36:51 CET 2014

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On 2/4/14, 1:29 PM, ibrahim khalil wrote:
> hi, i am new to gromacs. i was trying simulate multiple (eg. 3 or 4 ) carbon
> nanotubes in a single box. The way I am trying to do is …
> 1. Take both pdb files, merge them(using pymol) according to my orientation
> and create a single pdb file for the whole structure.
> 2. Generate the gro and hence the topology file using the forecfield I used
> to simulate a single cnt.
> 3. Run the mdrun program.
> I was wondering if there is anything wrong with this procedure.
> (I saw the posts for simulating multiple proteins in a single box and found
> it suggests simulating different proteins separately and then creating their
> topology files, converting them into .itp and then running the simulation)
> Also I am having some problems with the bonds. Whenever the CNTs are a
> little bit close[not too close to create a bond in between them], some
> unwanted bonds between two CNTs are created.
> it would be very nice if anyone could help me solve this problem.
> Thanks for your time.
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/bonding-problem-in-simulating-multiple-objects-in-the-same-box-tp5014293.html
> Sent from the GROMACS Developers Forum mailing list archive at Nabble.com.


Justin A. Lemkul, Ph.D.
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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