Re: Is there really no way of automating pair interaction calculations without invoking NAMD for each pdb file separately?

From: Nielsen, Steven (
Date: Thu Nov 01 2018 - 12:30:21 CDT

Clever use of namdenergy will do it. You would run a full simulation and then feed the trajectory (dcd) file to a tcl script invoking the namdenergy command.

On Nov 1, 2018, at 11:46 AM, Asghar Razavi <<>> wrote:

Dear all,

It is my understanding that to calculate pair interaction energies you would need to create a pdb file that specifies which atoms need to be used for energy calculations. If I want to calculate interaction energies for e.g. 100 pairs, I would need 100 pdb files.

Instead of creating 100 NAMD input files and invoking NAMD 100 times, I have been trying to adjust the following script to automatically load each pdb file and do the calculations. However, I get the error:

TCL: Setting parameter coordinates to C_10_15.pdb

FATAL ERROR: Setting parameter coordinates from script failed!

I have noticed that other people in the past have been experiencing similar problems when trying to automate the procedure. Does anyone have a better/faster way of doing these calculations or know how to adjust the following script to make calculations automated?

Thank you very much,


structure wt.psf

paraTypeCharmm on

parameters par_all36_prot.prm

parameters par_all36_lipid.prm

parameters par_water_ions.prm

numsteps 1

exclude scaled1-4

outputname namd-temp

temperature 0

COMmotion yes

cutoff 12

dielectric 1.0

switchdist 10

pairInteraction on

pairInteractionGroup1 1

pairInteractionGroup2 2

pairInteractionSelf off

for {set i 14} {$i < 18} {incr i} {

    coordinates C_10_$i.pdb

    pairInteractionFile C_10_$i.pdb

    coorfile open dcd tmp_10.dcd

    set ts 0

    while { ![coorfile read] } {

        firstTimestep $ts

        run 0

        incr ts 1


    coorfile close


Asghar Razavi
Postdoctoral Associate
Department of Physiology and Biophysics

Weill Cornell Medical College (WCMC)
1300 York Avenue, Room C505

New York, NY 10065<,+room+c503+new+york,+ny+10065>

Website: <>

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