[gmx-users] centering molecule in the water box
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
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.
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Lehrstuhl fuer Thermische Verfahrenstechnik
Phone: +49(0) - 9131 - 85 27671
Mailto: peyman.yamin at cbi.uni-erlangen.de
More information about the gromacs.org_gmx-users