[gmx-users] Query on restraining center of mass of a protein
Mark.Abraham at anu.edu.au
Tue Nov 15 01:39:13 CET 2011
On 15/11/2011 10:21 AM, Sanku M wrote:
> 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?
> 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 ?
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