[gmx-users] simulating multiple molecules in a box

Mark Abraham mark.j.abraham at gmail.com
Mon Feb 3 00:47:34 CET 2014

On Sun, Feb 2, 2014 at 8:28 PM, ibrahim khalil <
ibrahim.khalil.chem at gmail.com> 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)

For grompp, you need a topology that matches your input coordinates. How to
generate each depends very much on the contents of the system, because
different tools are available for proteins vs things like nanotubes. Those
posts were probably referring to using pdb2gmx to generate topologies for
each protein that could then be merged. You may not have that problem.

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.

Maybe it's not a problem. See


> Thanks for your time.
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