On 15/11/2011 10:21 AM, Sanku M wrote:
Hi,
I have a system containing water and a large protein. In the
simulation, I do not want the protein center of mass to drift away.
Why do you want it not to drift away? There's nothing magical about the
center of a periodic simulation cell. Why do you want to change the
dynamics to achieve this?
Mark
I was wondering what will be the reasonable method in gromacs to fix
the position of the center of mass of the protein in its original
position . I was thinking about two options in gromacs.
1) use the protein as comm-grp only to remove its center of mass
motion . ( or should I use both protein and non-protein ( water)
center of mass as comm-grps separately ).
2) Finding the residue closest to center of mass of the protein (
but I am not sure how to do it ).
Can anyone suggest which will be a good idea ?
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
