Evaluate energy of "protein + two closest ions"

From: Xiaodong Pang (xiaodong0119_at_gmail.com)
Date: Tue Aug 06 2013 - 17:25:45 CDT

Hi everyone,

I am trying to calculate the energy of "protein + two closest ions" when
running simulations.

I know "namdenergy" is able to do this AFTER I have the trajectory, and the
"pair interaction calculations" allows for the calculation of a group of
predefined atoms

However, the "two closest ions" needs to be specified every time step,
which can not be predefined.

Any suggestions?

Thank you!

-Xiaodong

+++++++++++++++++++++++++++++
 Institute of Molecular Biophysics,
 Physics Department,
 Florida State University,
 Tallahassee, FL 32306
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