Evaluate energy of "protein + two closest ions"

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

• Next message: Norman Geist: "AW: Colvar cannot be ran on supercomputer newton"
• Previous message: Norman Geist: "AW: Colvar cannot be ran on supercomputer newton"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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
+++++++++++++++++++++++++++++

• Next message: Norman Geist: "AW: Colvar cannot be ran on supercomputer newton"
• Previous message: Norman Geist: "AW: Colvar cannot be ran on supercomputer newton"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:30 CST