From: Kamp, Marc vander (Marc.vanderKamp_at_wur.nl)
Date: Mon Jun 21 2004 - 04:20:26 CDT
Dear all,
I would like to run several phases of minimization and equilibration in 1 configuration-file, see the execution part of the conf-file below.
My problem is that after the first short MD-phase in which harmonic constraints are applied, I want to set the constraints off for the next phase. I tried to do this by simply putting 'constraints off' before the next 'run' command, but namd stopped running reporting the following error in the log-file:
TCL: Setting parameter constraints to off
FATAL ERROR: Setting parameter constraints from script failed!
How should I correctly set the constraints to off for the next MD-run in the script?
Thanks in advance,
Marc
Here's the execution part of the conf-file:
### Minimization with protein backone fixed ###
fixedAtoms on
fixedAtomsFile fix_backbone.pdb
fixedAtomsCol B
minimize 2000
### Minimization without fixing atoms ###
fixedAtomsForces on
fixedAtoms off
minimize 2000
### Heating to set temperature with harmonic constraints on CA ###
# (NO pressure control!)
# re-initialize velocities after minimization to 50K
#reinitvels 50
# Heat to $temperature with 25K every 0.5 ps (takes 5 ps to reach 300K)
reassignTemp 50
reassignFreq 250
reassignIncr 25
reassignHold $temperature
# Harmonic restraints on CA atoms
constraints on
consRef restrain_ca.pdb
consKFile restrain_ca.pdb
consKCol B
run 5000 ;# 10 ps, 300K is reached after 5 ps
### Equilibration phase CPT - strict temperature control ###
### Using Langevin Temperature control and Nose-Hoover Langevin piston pressure control
constraints off
# Constant temperature control
langevin on
langevinDamping 5 ;# 5/ps damping coefficient
langevinTemp $temperature
langevinHydrogen no ;# don't couple bath to hydrogens
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no ;# no for waterbox, yes for membrane
useConstantArea no ;# no for waterbox, maybe for membrane
langevinPiston on
langevinPistonTarget $pressure
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
run 20000 ;# 40 ps
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