[gmx-users] how to prepare implicit solvent system??

[Justin A. Lemkul]

김현식 wrote:
> If i want to use implicit solvent, genbox step is indispensable ?
> or Just GBSA in mdp file can effect like solvation ?
> 

It sounds like you need to do a bit of literature/textbook reading before you 
continue.  If you're using implicit solvent, then you don't need explicit 
solvent.  That's sort of the point.

-Justin

>  > Date: Tue, 19 Apr 2011 09:49:25 -0400
>  > From: jalemkul at vt.edu
>  > To: gmx-users at gromacs.org
>  > Subject: Re: [gmx-users] how to prepare implicit solvent system??
>  >
>  >
>  >
>  > 김현식 wrote:
>  > > Dear experts,
>  > >
>  > > hi, I'm using Gromacs for implicit solvent system, Can anybody let me
>  > > know hot to prepare the implicit solvent system??
>  > >
>  >
>  > Just as you would any other system, except you don't need to define a 
> unit cell
>  > full of water and ions. pdb2gmx, grompp, mdrun. There are benchmarks and
>  > example input files on the Gromacs site.
>  >
>  > -Justin
>  >
>  > > Thanks
>  > >
>  >
>  > --
>  > ========================================
>  >
>  > 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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-- 
========================================

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

========================================