[gmx-users] How to run solvation dynamics for some organic molecules

lina lina.lastname at gmail.com
Fri Aug 5 16:53:52 CEST 2011

On Fri, Aug 5, 2011 at 7:23 PM, Ravi Kumar Venkatraman
<ravikumarvenkatraman at gmail.com> wrote:
> Dear all,
>              I have generated .gro and .top file for Chloranil from prodrg
> and tried solvate it using pre-equilibrated cyclohexane. When i tried to
> generate the box containing solute it is not modifying the .top file and it
> shows zero solvent.
> Please help me how to solvate organic molecules that are obtainde from
> prodrg.
> Thank you.


genbox -cp chloranil.gro -cs cyclohexane.gro -o system.gro

and manually modify the topol.top later.

you may use the solvated pre-equilibrated cyclohexane as
cyclohexane.gro, so no need add water later.

It should be no problem.
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Best Regards,


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