[gmx-users] box volume

Vitaly V. Chaban vvchaban at gmail.com
Sat Aug 29 22:38:13 CEST 2015

Yes, you should.

Your system volume should allow the nanotube and the polymer to be
completely solvated once separated.

Good luck.

On Sat, Aug 29, 2015 at 8:08 AM, soumadwip ghosh
<soumadwipghosh at gmail.com> wrote:
> Hi,
>     beg me pardon if my question appears very silly to you. I have a hybrid
> of a Carbon nanotube and a polymer and I want to study the unwrapping
> dynamics of the polymer in presence of a polymer binding agent. I kept the
> hybrid inside a triclinic box and am doing simulations in presence of that
> binder for 100 ns. The size of the box is around 277 nm3. Is there a
> possibility that once the hybrid dissociates the polymer may not have
> enough volume to go apart from the CNT and hence affecting the correct
> dynamics picture? Should I perform such kind of simulations in a bigger
> box? I might be missing out something very fundamental. Your help would be
> appreciated.
> Sorry if I am asking for much.
> Soumadwip Ghosh
> Research Fellow
> Mumbai
> India
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