[gmx-users] Center of mass distance
Mark.Abraham at anu.edu.au
Fri May 5 06:24:49 CEST 2006
YOLANDA SMALL wrote:
> 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...
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