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

[Justin A. Lemkul]

Matthias Schmidt wrote:
> Hi,
> 
> genbox can now modify the topology file by using genbox ... -p topol.top.
> 

This still only works for SOL entries, as of the latest release-4-5-patches.  It 
would be quite useful if the topology could be updated for any arbitrary 
solvent, but at present, is still limited.

-Justin

> Best,
> 
> Matthias Schmidt
> 
> On Friday, August 5, 2011, lina <lina.lastname at gmail.com 
> <mailto:lina.lastname at gmail.com>> wrote:
>  > On Fri, Aug 5, 2011 at 7:23 PM, Ravi Kumar Venkatraman
>  > <ravikumarvenkatraman at gmail.com 
> <mailto: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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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