[gmx-users] (no subject)

[J Lorieau]

Hi Anton,

	Molecules are suppose to diffuse. It wouldn't be a problem in my
simulation if I had a very big box. However, my HIV protease drift right
out of the box. This causes it to drift out of the solvent, and it
causes one of the sub-units to fly to the other side of the box - which
rips my protein apart. I've tried comm_mode=linear, but it doesn't work.

Justin

On Tue, 2002-07-16 at 08:50, Anton Feenstra wrote:
> Alan Wilter Sousa da Silva wrote:
> > 
> > On 15 Jul 2002, David wrote:
> > 
> > > On Mon, 2002-07-15 at 20:26, J Lorieau wrote:
> > > > Hi,
> > > >
> > > >     I have a simple question, unfortunately. I'm simulating 1A30 - HIV
> > > > protease in box of water. HIV PR is a dimer. After about 1 ns of
> > > > simulation, the protein COM drift out of the box.
> > > This is not a problem, but if you really don't want it to happen you can
> > > apply center-of-mass motion removal to your protein and solvent
> > > separately if you wish by specifying com-groups.
> > 
> >         I have a system with protein + inhibitor + ions + solvent, should
> > I apply so center-of-mass motion removal to each group in order to avoid
> > such COM drift?  Or just protein and solvent?
> 
> Sorry for maybe sounding a bit sarcastic, but molecules diffuse, 
> don't they? So, what is the big deal? The are *supposed* to diffuse.
> You should have a very good reason to stop them from doing that.
> 
> If you want to look at the dynamics of your solute (without solvent)
> and don't want to see it diffusing, you can always tell trjconv to 
> remove jumps and center the system for you (trjconv -center -pbc
> nojump).
> Use -fit if you also want to get rid of overall rotation of the solute.
> 
> >         The mdrun -rerun will not have result, won't it?
> 
> No, it won't. It just re-calculates properties (energies, mainly) 
> from an existing trajectory.
> 
> -- 
> Groetjes,
> 
> Anton
>  ________ ___________________________________________________________
> |        | Anton Feenstra                                            |
> | .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
> | |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
> | |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
> | ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
> |  /  \  |-----------------------------------------------------------|
> | (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
> |  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
> |   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
> |  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
> | (    ) |-----------------------------------------------------------|
> |  \__/  | "Right Now My Job is Eating These Doughnuts" (Bodycount)  |
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-- 
Justin Lorieau 
          Biophysical Chemist
          Department of Chemistry 
          Columbia University 
          3000 Broadway Avenue, MC 3162 
          New York, NY 10027 
          USA 
	  
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