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

[Matthias Schmidt]

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.
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> Best Regards,
>
> lina
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>

-- 
Best,

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

http://sbcb.bioch.ox.ac.uk/schmidt.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110806/8c6d625f/attachment.html>