Re: Force Calculation in NAMD

From: Gadi Oron (gadi_at_proteologics.com)
Date: Sun May 23 2004 - 02:37:27 CDT

Hi,

On Fri, 2004-05-21 at 21:02, Xin Chen wrote:
> Hi,
>
> I want to get force between every atoms or residues at certain time of
> simulation, anyone knows how to do it in NAMD? That is, I want the force
> between atom i and atom j, or between residue i and residue j. Thanks.

You should run your simulation normally, and then run on the DCD and
extract the info using PairInteraction.

I've included a perl script and a namd config file the do just that.

You should take a look at the pairs.namd and edit it to suite your own
parameters, then run

energy_matrix.pl SEG1:ST1-END1 SEG2:ST2-END2

This will calculate the interaction energies between all the residues in
segment SEG1 from residue ST1 up to END1 with the residues in segment
SEG2 from residue ST2 up to END2. It gives both the average and the
standard deviation of the energy.

You should have PDL installed.

Hope that helps.

-- 
================= Gadi ORON, PhD -o- Proteologics ======================
========== gadi/at/proteologics.com ========== +972 8 9475666 ==========
Dr. Jekyll had something to Hyde.
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## Author: Gadi Oron
## gadi_at_proteologics.com

# initial config
coordinates complete.pdb
temperature 0

# output params
outputname pair-analyze
binaryoutput no

# integrator params
timestep 1

structure complete.psf
## force field
##############
paratypecharmm on
parameters ../par/par_all27_prot_lipid.inp
parameters ../par/par_unbonded_zincs.inp
parameters ../par/par_SO4.inp

exclude scaled1-4
1-4scaling 1.0

## approximations
#################
switching on
switchdist 8
cutoff 12
pairlistdist 13.5
margin 1
 
# Atom in group 1 have a 1 in the B column; group 2 has a 2.
pairInteraction on
pairInteractionFile pair_tmp.pdb
pairInteractionCol B
pairInteractionGroup1 1
pairInteractionGroup2 2

set ts 0

coorfile open dcd out/run_out.dcd

# Read all frames until nonzero is returned.
## Use:
## while { ![coorfile read] && $ts < 100 } {
## to run only on the first 100 frames
while { ![coorfile read]} {
  # Compute energies and forces, but don't try to move the atoms.
  run 0
  incr ts 1
}
coorfile close

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