[gmx-users] Removing Rotation and Translation

Alan Wilter Sousa da Silva alan at biof.ufrj.br
Tue Jul 16 18:24:30 CEST 2002

Thanks for your attention.

	I agree when you say that molecules must diffuse and that's what
I set to my protein systems.
	However we had a similar problem with micelles as described by
Justin and unfortunately your suggestion with trjconv didn't work as
	Nevertheless I hope you Justin can try it and I would appreciate
very much if you report us how it did.

	Just an observation, -pfit could be more interesting but it doesn't
work well with -pbc nojump option (my dimer has its chains broken apart).
Anyway, just -pfit and selecting only protein works pretty well.

 Justin wrote:
>        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.

David wrote:
> You want the ions to diffuse around freely, unless they are tightly
> bound to the protein. Usually your inhibitor is also tightly bound.
> Everything that should stick to the protein should be in one COM group,
> while the rest (solvent + counter ions) should be in the other.

On Tue, 16 Jul 2002, 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.

Alan Wilter S. da Silva
 Laboratório de Física Biológica
  Instituto de Biofísica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil

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