[gmx-users] simulation of the protein in vacuum

[David van der Spoel]

On Wed, 2005-01-12 at 09:49 -0200, Alan Wilter Sousa da Silva wrote:
> David wrote:
> >set all cutoffs to zero, nstlist = 0 and use comm-mode = angular
> 
> Nice, so, GMX won't mind about PME, RF etc. automatically, right? And I 
> should use GROMOS96 43b1 Vacuum Forcefield (official distribution), ok?
You can also use OPLS, but you probably want to neutralize most
sidechains in pdb2gmx (this is the difference between gromos solvent and
vacuum force fields)
> 
> Cheers,
> Alan
> 
> --------------------------
> Alan Wilter Sousa da Silva
> --------------------------
> D.Sc. - IBCCF/UFRJ
> Projeto BioPAUA - HP/LNCC
> Petrópolis (RJ), Brasil
> www.lncc.br/~alan
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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