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
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