From: Shunzhou Wan (
Date: Wed Dec 10 2003 - 11:23:46 CST

Hi namd users,

I want to use the Pair Interaction Calculation feature in namd 2.5 to
calculate the interaction energy of solute and solvent. I did some
periodic simulations at constant pressure. I have some questions about
coorfile command:

1. I don't think the interaction energies/forces should depend on the
extendedsystem (to read cell parameters) and useGroupPressure commands
because the cell informations are in the coordinate dcd file and they
are updated every step. However, my results shown the energies and
forces are dependent on these two commands. In addition, when
extendesystem is active, the forces are dependent on the dcdunitcell
command, although the energies are same. I wonder how to choose these
options. Part of my configuration file is:
extendedSystem md1.xsc # use it or not

useGroupPressure on #
use it or not
BerendsenPressure on #
use it or not
BerendsenPressureTarget 1.01325 # use it or
BerendsenPressureCompressibility 0.0000446 # use it or not
BerendsenPressureRelaxationTime 200.0 # use it or not
BerendsenPressureFreq 1 # use
it or not

dcdunitcell yes (no)
   # use yes or no

pairInteraction on
pairInteractionFile pair.pdb
pairInteractionCol X
pairInteractionGroup1 1
pairInteractionGroup2 2

set ts 500

coorfile open dcd md.dcd
while { [coorfile read] != -1 } {
   firstTimestep $ts
   run 0
   incr ts 500

coorfile close

2. If my dcd file dosen't contain the cell information, is it possible
to read them from the XST file? Or how can I add cell informations to
dcd file?

I would appreciate if anyone could help me with this.

Shunzhou Wan

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:13 CST