Read dcd file and calculate (distance/constraint energy Vs snapshots) using NAMD

From: priyodorshi satpati (psatpati_at_gmail.com)
Date: Wed Nov 04 2009 - 11:05:33 CST

Dear all,

 I have a NAMD traj file (dcd) of a solvated Mg+HPO4 system. Two separate
harmonic springs are attached to Mg and P relative to some reference
positions of Mg and P respectively.

I want to read the traj file using *a NAMD script *and want to get the
following data

*(Mg-P distance+coordinates of Mg and P+total restraint energy) Vs
(snapshots)*

The following lines (in my NAMD config file) are able to read the dcd traj
but I am not able to extract the desired data.
##############################
dcdunitcell yes
set ts 1
coorfile open dcd $inputname.dcd

while { [coorfile read]!= -1 } {
firstTimestep $ts
run 0
incr ts 100
}
coorfile close
##############

Please suggest me to get my desired data's from the loop using NAMD script.
Though It can be done using VMD but i want to do it by NAMD.

Thanks

Regards

satpati

-- 
Dr. Priyadarshi Satpati
Biocomputing and Structure research Group,
Laboratoire de Biochimie,
Ecole Polytechnique,
91128 Palaiseau, France
Phone :
         (Off)  : +33/(0)1 69 33 48 94
         (Mob) : +33/(0)6 27 75 56 49
         (Res) : +33/(0)177069139

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