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: jalem...@vt.edu
> To: gmx-users@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
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