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!


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

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