Re: Tcl script in NAMD

From: Jim Phillips (
Date: Tue Oct 19 2010 - 11:49:16 CDT

You can only read new coordinates, not change which atoms you are
calculating interactions between. You would need to invoke NAMD
separately for each input PDB file to do it as you describe.

A much better solution would be to set up a system with only two water
molecules in the same size box, and then use VMD to write a 6-atom dcd
file where each frame is a different pair of water molecule coordinates.


On Tue, 19 Oct 2010, divya nayar wrote:

> Hi,
> 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
> command.
> 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
> dcd?
> I will be really grateful to you if you can help me with this.
> Thanks,
> Divya

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