[gmx-users] [gmx-developers] bonding problem in simulating multiple objects in the same box
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.
Department of Pharmaceutical Sciences
School of Pharmacy
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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