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

Matthias Schmidt matthias.rene.schmidt at gmail.com
Sat Aug 6 02:17:28 CEST 2011


Hi,

genbox can now modify the topology file by using genbox ... -p topol.top.

Best,

Matthias Schmidt

On Friday, August 5, 2011, lina <lina.lastname at gmail.com> wrote:
> 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 p
re-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.
>
>
> Try:
>
> 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,
>
> lina
> --
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-- 
Best,

Matthias
-- 
Structural Bioinformatics and Computational Biochemistry Unit
Dept. of Biochemistry
University of Oxford

http://sbcb.bioch.ox.ac.uk/schmidt.php
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