changing harmonic restraints (colvars)

From: Jon Phillips (pcxjp3_at_nottingham.ac.uk)
Date: Thu Apr 05 2012 - 06:52:46 CDT

Hi,

I'm trying to create a homology model of a protein bound to a ligand.
I've generated a (bad) starting structure, and am trying to use harmonic
restraints to pull the ligand into a more realistic configuration.

First I added one restraint in which I dropped a distance (d) from
6.695159 to 2.0, but now when I try to restart the run and add a new
colvar (f) namd throws errors at me.

If I just add an extra colvar to the file, I get this:

colvars: Restarting from file "res/play2_res.colvars.state".
colvars: Restarting collective variable "d" from value: 2.09068
colvars: Error: in reading restart configuration for collective
variable "f".
colvars: If this error message is unclear, try recompile with
-DCOLVARS_DEBUG.
FATAL ERROR: Error in the collective variables module: exiting.

If I try to ignore the restart, so comment out the line containing
colvarsInput from my configuration file, I get:

FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

This happens almost immediately (if I tell it to write to the dcd at
every step I get one frame).

Before anybody starts telling me about margins and sizes of box, I don't
get either errors if I:

a) turn colvars off entirely
b) use the original restraints
c) don't add the new colvar (f) and use colvarsInput

I do still get the error if I turn margins up to 75 (which is roughly
the size of my box), and a quick inspection shows that the box shouldn't
change much - it's the same size as it's contents and I can't see any
gaps.

My configuration file is:

###############################################################################
set temperature 298
# Input
paraTypeCharmm on
parameters /mnt/beagle.tmp/jp.beagle/computations/toppar/par_all22_prot_cmap_mas_namd.inp
parameters /mnt/beagle.tmp/jp.beagle/computations/toppar/cgenff2b7/par_all36_cgenff_namd.prm
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# SHAKE on all H-containing bonds incl. both O-H water
bonds - needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control

#temperature $temperature
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Output
restartsave yes
binaryrestart yes
restartfreq 50000 ;# 250=0.5ps, 2500=5ps, 25,000=50ps, 250,000=0.5ns
dcdfreq 1000
outputEnergies 500
outputPressure 500
# Setting up PBC for an octahdron box with NAMD
set a 75.334
set b [expr $a/2]
cellBasisVector1 $a 0 0
cellBasisVector2 $b $b $b
cellBasisVector3 $b -$b $b
cellOrigin 0 0 0
wrapAll on
wrapNearest on
PME yes
PMEGridSpacing 1
useGroupPressure yes
useFlexibleCell no
useConstantArea no
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
binaryoutput no
structure rabbit_2gdc_struct3fh_molprob_pdbv3_solv-octa_xplor.psf
bincoordinates res/play2_res.50000.coor
binvelocities res/play2_res.50000.vel
coordinates eqm/play2.coor
extendedSystem res/play2_res.50000.xsc #eqm/play2.xsc
set outputname eqm/play2more2
firsttimestep 0
colvars on
colvarsConfig distance_restraint2.in
colvarsInput res/play2_res.colvars.state
#temperature $temperature
# Output
outputName $outputname
restartName res/play2more2.res
margin 5 #Allows volume to change when moving from NVT to NPT
langevinPiston on
constraints off
run 50000 ;#1000ps equilibration
puts [format "STATUS: Heating stage complete"]

###############################################################################

The colvars file on my last run was:

#TrajFrequency 100
colvarsRestartFrequency 10000
colvar {
name d
distance {
group1 {
atomNumbers 1608
}
group2 {
atomNumbers 2025
}
}
}
harmonic {
colvars d
centers 6.695159
targets 2.0
targetsnumsteps 50000
forceConstant 25.0
forceConstantTarget 25.0
}

And this time I'm aiming for:

#TrajFrequency 100
colvarsRestartFrequency 10000
colvar {
name d
distance {
group1 {
atomNumbers 1608
}
group2 {
atomNumbers 2025
}
}
}
colvar {
name f
distance {
group1 {
atomNumbers 2096
}
group2 {
atomNumbers 1237
}
}
}
harmonic {
colvars d
centers 2.0
targets 2.0
targetsnumsteps 50000
forceConstant 25.0
forceConstantTarget 25.0
}
harmonic {
colvars f
centers 13.81
targets 2.0
targetsnumsteps 50000
forceConstant 25.0
forceConstantTarget 25.0
}

Any help would be appreciated.

Jon Phillips

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