[gmx-users] implicit solvent system set up

[Justin A. Lemkul]

E. Nihal Korkmaz wrote:
> Dear all,
> 
> This may sound stupid, but just to make sure that I am right track about 
> implicit solvent simulations, the set up involves
> pdb2gmx
> editconf
> grompp
> 
> I mean, we still need to define the box dimensions by editconf and apply 
> periodicity, right?

Not usually.  Proper settings usually include "pbc = no" and long cutoffs.  This 
has been discussed at length in the list archive.

> Besides, what type of ensemble would be a good choice (NPT, NVT, etc)?
> 

Typically NVT.  There is nothing compressible for NPT to act upon - you have, 
e.g., a protein in an imaginary bath of solvent.  If you apply NPT conditions, 
the box will just collapse in on itself.

-Justin

> Best,
> 
> -- 
> Elif Nihal Korkmaz
> 
> Research Assistant
> University of Wisconsin - Biophysics
> Member of Qiang Cui & Thomas Record Labs
> 1101 University Ave, Rm. 8359
> Madison, WI 53706
> Phone:  608-265-3644
> Email:   korkmaz at wisc.edu <mailto:korkmaz at wisc.edu>
> 
> 

-- 
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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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