VMD-L Mailing List

From: Ivan Degtyarenko (imd_at_fyslab.hut.fi)
Date: Mon Aug 21 2006 - 08:26:44 CDT

Dear All, if someone has any experience and could share it, I'd really
appreciate. I'm in process of analyzing the molecular dynamics trajectory,
the ion solvated in water, and may be somebody has ready solutions, just
to save time and do not reinvent the wheel. I'm looking for the next VMD
scripts:

# The first one, which would load a trajectory, go through all frames
centering them by the center of mass (whole system or some particular
selection) and save the trajectory to a new file.

# The second script, which could compute the average residence time of
hydrogen bonds between the ion and water molecules.

# The third one, which would output the abundance of coordination numbers
of the ion atoms.

It would be great to see some code examples, thanks a lot in advance,

YT, Ivan Degtyarenko