can the harmonic constraint parameters be changed between run or minimize?

From: Chongbo Sun (chongbo_at_ualberta.ca)
Date: Sun Nov 23 2008 - 14:03:39 CST

Hello NAMD users,

Can the harmonic constraint
parameters(consref,conskfile,constraintScaling) be changed between
'run's or 'minimize's?
e.g., Will the following conf file(part of it) work?
"
constraints on
consref om-0.pdb
conskfile consk-1.pdb
conskcol B
constraintScaling 50

minimize 100

consref ref-1.pdb
conskfile consk-222.pdb
conskcol B
constraintScaling 50

minimize 100

constraints off
minimize 500

constraints on
consref ref-222.pdb
conskfile consk-33333.pdb
conskcol B
constraintScaling 5

run 2000

constraints off
run 200000
"
And do all the consref, conskfile pdb files need to have all the atom
lines as the "coordinates" pdb file?
Or I only need to put the atoms need to be restraint into "consref,
conskfile" pdb files?
Can I use binary format for consref, conskfile pdb?

Thanks!
Chongbo

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