[gmx-users] simulation of the protein in vacuum

Alan Wilter Sousa da Silva alan at lncc.br
Wed Jan 12 17:31:51 CET 2005

Actually, to be more specific about MD in vacuum, why (in mdp file)
comm_mode=Angular? Just to remind me, but I think it concerns about PBC, 
doesn't it?

A observation, when using genion:

WARNING: turning of free energy, will use lambda=0
(should be tuning *off* ?)


On Wed, 12 Jan 2005, 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?

Alan Wilter Sousa da Silva
Projeto BioPAUA - HP/LNCC
Petrópolis (RJ), Brasil

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