AMBER Archive (2001)

Subject: Following Coordinates

From: Troy Bothwell (tbothwe1_at_bigred.unl.edu)
Date: Wed Apr 04 2001 - 18:23:16 CDT

Hello all,

What is the most straight forward way to get the coordinates of a selected
subset of atoms. Is this most easily performed post dynamics or is there a
way to dump the coordinates during the simulation? I need to follow 6-10
atoms.

Here is another related question. I see that in ptraj I can do the distance
and angle between selected atoms. I assume that the atoms in the "mask"
don't have to be consecutive (i.e. they can be in vastly different parts of
the molecule).

Thanks for your time,

Troy