[gmx-users] How to simulate spc216.pdb in different water potentials

[Justin A. Lemkul]

Ravi Kumar Venkatraman wrote:
> Dear Sir/ Madam,
>                           I would like to run simulation for water in 
> different water potentials like spc spc/e tip3p tip4p ... But when I do 
> pdb2gmx and genbox to solvate the box (l= 1.862) I am not able generate 
> box of 216 molecules. Please find me a solution.
> 

You don't need pdb2gmx.  All the coordinate and topology files are already 
provided in $GMXLIB or the force field subdirectories.  Write the system .top 
with a text editor, generically:

#include "forcefield.itp"
#include "water.itp"

[ system ]
water

[ molecules ]
SOL 216

-Justin

> Thank you in advance
> 
> *With Regards,**
> *
> *
> *
> *Ravi Kumar Venkatraman,*
> *c/o Prof. Siva Umapathy,**
> *
> *IPC Dept., IISc.,*
> *Bangalore, INDIA.*
> *Phone No: +91-9686933963*
> 

-- 
========================================

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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