Tcl script in NAMD

From: divya nayar (
Date: Tue Oct 19 2010 - 08:21:48 CDT

I have some doubt regarding the usage of Tcl script in NAMD. I have been
using the tcl scripting to calculate the Pair Interaction between atoms
using the script given in NAMD User's guide by making use of coorfile

set ts 100
coorfile open dcd ../tip4p-prod260.dcd

while {! [coorfile read] } {
   firstTimestep $ts
   run 0
   incr ts 100
coorfile close

Now I want to carry out the calculation of Pair Interaction using pdb files
(PairInteractionFile) which change with loading of each frame from dcd file.
e.g. I have a system of 256 molecules of water in a cubic box. I want to
find the Pair Interaction between each water molecule with the others. So I
create 256 pdb files with waters tagged accordingly in beta-column of pdb
files and do the run. Now, I want to calculate the Pair Interaction betwen
particular set of indices which are changing with each frame of dcd. It is
not a good method to first generate say 10000 pdb files (when total no. of
frames are 10000). Is there a way in Tcl scripting by which I can tell NAMD
conf file to change the pdb files as and when the new frame is loaded from

I will be really grateful to you if you can help me with this.


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