[gmx-users] Query on restraining center of mass of a protein

Mark Abraham Mark.Abraham at anu.edu.au
Tue Nov 15 01:39:13 CET 2011

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?


> 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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