pair Interaction Calculation

From: Ioana Cozmuta (
Date: Thu Oct 16 2003 - 17:36:18 CDT

Hi namd users,

I want to use the Pair Interaction Calculation feature in namd 2.5 but I
seem not to be able to figure out the right way to do it.

I want to get forces on group 1 from interaction with group 2 calculated
from a dcd trajectory. The manual says to set "run 0" so that NAMD does
NOT run any dynamics but only prints the energies/forces. However I want
NAMD to print the energies/forces at every time step existing in the
trajectory file. The problem is that it's only giving me the output for
the first step.
I would appreciate if anyone could help me with this.
 I am using the configuration file below.

Thank you,


# force field params
exclude scaled1-4
1-4scaling 0.8333
scnb 2.0
amber on
parmfile ./pore1Kspcm.prmtop
coordinates ./EqSPMK90.coor
temperature 300
seed 314159
switching on
switchdist 17.5
cutoff 18.5
pairlistdist 20.0
margin 0.0
rigidBonds all
timestep 2
nonBondedFreq 2
fullElectFrequency 4
stepsPerCycle 20
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile ./fix_pore_1Kfree.pdb
fixedAtomsCol B
pairInteraction on
pairInteractionFile ./pairInt_Kprot.pdb
pairInteractionCol B
pairInteractionSelf off
pairInteractionGroup1 3
pairInteractionGroup2 2
outputname results
run 0

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