pair interactions in NPT

From: Anna Modzelewska (
Date: Thu Sep 01 2005 - 03:21:46 CDT

I need to calculate pair interaction energy after a simulation in NPT. For each sets of coordinates from a dcd file I have different sets of CellBasisVectors. I took the script below and I adopted it in the way that it changes not only the fistTimestep but also the CellVectors. It didn't work!
After several modifications I discovered that NAMD can not change vectors values during a simulation (it stops with information "FATAL ERROR: Setting parameter cellBasisVector1 from script failed").
I absolutely need to calculate the interaction energy for my simulations, what can I do?

Any help will be very appreciated!

"coorfile open dcd name.dcd

set ts 0
while { [coorfile read] != -1 } {
  incr ts
  firstTimestep $ts
   run 0
coorfile close"

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:06 CST