rotating constraints

From: himanshu chandola (
Date: Tue Nov 18 2003 - 20:17:14 CST

    I used namd's rotating constraints feature by specifying the
parameters for rotating constraints. NAMD's user guide is not clear on how
to specify the spring constants and the file containing them - so i used
the same notation for them as used for harmonic constraints.

After incorporating them i got the following warnings - showing that my
rotating constraints were not used in the simulation:

Warning: The following variables were set in the
Warning: configuation file but were not needed
Warning: conskfile
Warning: conskcol
Warning: rotConstraints
Warning: rotConsAxis
Warning: rotConsPivot
Warning: rotConsVel

Added below is the configuration file i used.

Has anybody used rotating constraints before ?


structure pro.psf
coordinates pro_eq.pdb
paratypecharmm on
parameters par_all22_prot.inp
timestep 1
cutoff 17
switching on
switchdist 8
pairlistdist 18.5
exclude scaled1-4
temperature 0
restartname res_pro_rot
restartfreq 1000
fixedAtoms on
fixedAtomsForces off

fixedAtomsFile fixed.pdb
fixedAtomsCol B

#rotating constraints

rotConstraints on
rotConsAxis -3.253 98.41 -1.31
rotConsPivot 78.99 -9.76 142.43
rotConsVel 0.005
conskfile back_rot.pdb
conskcol B

outputname pro_rot
outputEnergies 1000

DCDfreq 200
DCDfile rot.dcd

run 48000

Morpheus: Do you believe in fate, Neo?
Neo: No.
Morpheus: Why Not?
Neo: Because I don't like the idea that I'm not in control of my life.

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