[gmx-users] (no subject)

[Anton Feenstra]

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                 |
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|  \__/  | "Right Now My Job is Eating These Doughnuts" (Bodycount)  |
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