[gmx-users] simulation of the protein in vacuum

[Kay Gottschalk]

to avoid the flying ice-cube:-) (i think...)

On Jan 12, 2005, at 6:31 PM, Alan Wilter Sousa da Silva wrote:

> 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* ?)
>
> Cheers,
> Alan
>
> 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
> --------------------------
> D.Sc. - IBCCF/UFRJ
> Projeto BioPAUA - HP/LNCC
> Petrópolis (RJ), Brasil
> www.lncc.br/~alan_______________________________________________
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Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Herzl St. 1
Rehovot
Israel
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