average position of water

From: Hungie Hungie <hungie01_at_hotmail.com>
Date: Tue 08 Jan 2002 19:28:00 +0700

Dear Amber user,

I have a trajectory of 100 ps MD simulation of a small DNA with explicit
solvent. The DNA was fixed during simulation (ibelly=1). My goal is to
equilibrate water positions.

I would like to determine something using coordinates of DNA and water
molecules. For the coordinations, I don't want to choose 1 snapshot from the
trajectory, however, I would like to use average position for the

Could anyone suggest me how to average position of waters?
I have tried to average by using ptraj with command "average" and I found
that some water molecules located within DNA. This may be water molecules
moved around DNA during simulation.

Many thanks in advance.


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Received on Tue Jan 08 2002 - 04:28:00 PST
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