From: Aron Broom (broomsday_at_gmail.com)
Date: Thu Apr 05 2012 - 10:01:16 CDT
I don't know about the margin thing, but in terms of the new colvar, you'll
need to manually edit the .colvars.state file you are using for restarting
in order to add that new colvar. Basically, your colvars config file no
longer matches the restart file. The .colvars.state file is human
readable, you just need to add in a few lines saying what your colvar is,
and what it's current value is, then it should work. I've done it before
when I've run metadynamics and then later stopped the metadynamics and used
umbrella sampling to smooth the PMF. If you can't figure out what the text
should look like, just start a fresh run with those colvars and run for 1
step and then have a look at the new state file.
~Aron
On Thu, Apr 5, 2012 at 7:52 AM, Jon Phillips <pcxjp3_at_nottingham.ac.uk>wrote:
> 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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-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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