[gmx-users] Center of mass distance

[Mark Abraham]

YOLANDA SMALL wrote:
> Hello,
> 
> I would like to determine the percentage of water occupation in a protein region
> by calculating the distance between the center of mass of a group of atoms and
> the solvent.  Does anyone know which gromacs tools can provide an estimate of
> this information?  By the way my trajectory is in xtc format.

Your trajectory format won't matter if there is a gromacs tool for the 
job because they all read and write all of them transparently.

However you need to define your problem better - you can't measure a 
distance between the center of mass of a group of atoms and "the 
solvent", which is a region of space. Nor can I see how this distance 
would help you calculate such a percentage of occupation. If you can 
write down an algorithm that will produce the result then you'll be 
closer to being in business...

Mark