[gmx-users] centering molecule in the water box

Peyman Yamin Peyman.Yamin at cbi.uni-erlangen.de
Tue Jul 1 12:38:47 CEST 2008

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. 


> The protein experience self-diffusion and so it moves through the
> simulation box.
> I tried also with editconf but the result is the same.
> F.
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Peyman Yamin
Lehrstuhl fuer Thermische Verfahrenstechnik
Universitaet Erlangen-Nuernberg
Egerlandstr. 3
91058 Erlangen
Phone: +49(0) - 9131 - 85 27671
Mailto: peyman.yamin at cbi.uni-erlangen.de

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