[gmx-users] centering molecule in the water box

Fabio Affinito affinito at sissa.it
Tue Jul 1 12:55:14 CEST 2008

the protein moves because the c.o.m. motion wasn't subtracted during  
the dynamics.

> On Tuesday 01 July 2008 12:24, Fabio Affinito wrote:
> I think if it moves, then there is something more basic wrong, do  
> you remove
> your center of mass motion appropriately? is your box homogeneously
> equilibrated? but if it does not move and it looks like as if it  
> moved, then
> it's visual problem and not important! you could e.g. write  
> something to cut
> the solvent molecules from one side and put them on the other side  
> with some
> mapping dependant on your box type, if you would like to see your  
> molecule at
> the center.
> btw, self diffusion is the diffusion of one molecule through others  
> of its own
> kind, not through other molecules, solvent or else. if there is no  
> chemical
> potential ( ~concentration ) difference, no mass transfer would take  
> place.
> Peyman

Fabio Affinito, PhD
SISSA/ISAS -Statistical and Biological Physics
Via Beirut, 4
34014 Trieste
email: affinito at sissa.it  phone:+39 040 3787 303  fax:+39 040 3787 528

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