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

ibrahim khalil ibrahim.khalil.chem at gmail.com
Tue Feb 4 18:43:52 CET 2014

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

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.

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