From: Jackson Cavett (jcavett_at_mail.bradley.edu)
Date: Tue Sep 13 2016 - 08:34:30 CDT
Hello NAMD Users,
I am attempting to heat a molecule from 10K to 310K over the course of a
few simulations. I put in the following parameters to accomplish this
heating:
reassignFreq 2
reassignTemp 10
reassignIncr 0.01
reassignHold 60
However, when I run the simulation, I get the periodic boundary error on
the first timestep. Here is the log file which shows the problem:
REINITIALIZING VELOCITIES AT STEP 100000 TO 10 KELVIN.
TCL: Running for 10000 steps
REASSIGNING VELOCITIES AT STEP 100000 TO 60 KELVIN.
PRESSURE: 100000 110.253 -0.316211 -6.80342 -0.316211 126.441 1.37312
-6.80342 1.37312 145.667
GPRESSURE: 100000 116.487 -0.516909 -5.56659 0.0868719 131.886 1.15381
-5.4699 1.44817 149.358
ETITLE...
OPENING EXTENDED SYSTEM TRAJECTORY FILE
REASSIGNING VELOCITIES AT STEP 100002 TO 60 KELVIN.
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.
I don't understand why the temperature is being reassigned to 60K when I
stated that it should be reassigned to 10K every two timesteps. Can anyone
explain what is happening here?
Here is the full configuration file I used. Please note what I did with the
binVelocities. I'm not sure if I can comment them out like that when I use
a restart file, so please let me know what I should do with that. The
reason I comment it out is that I want to set the temperature of my
simulation while still using a restart file.
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Equilibration of alphVbeta3 after minimization
# Shorter simulations so dcd can be analyzed
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ../alphaVbeta6_wb.psf
coordinates ../alphaVbeta6_wb.pdb
set temperature 10
set outputname beta6_equil_1
# Continuing a job from the restart files
if {1} {
set inputname ../minimization/beta6_min_fixed_protein
binCoordinates $inputname.restart.coor
#binVelocities $inputname.restart.vel
extendedSystem $inputname.xsc
}
firsttimestep 100000
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters ../par_all27_prot_lipid.inp
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1. ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
cellBasisVector1 121 0.0 0.0
cellBasisVector2 0.0 93 0.0
cellBasisVector3 0.0 0.0 57.5
cellOrigin 20.045 -30.903 25.591
wrapWater on
wrapAll on
wrapNearest off
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0
#manual grid definition
#PMEGridSizeX 45
#PMEGridSizeY 45
#PMEGridSizeZ 48
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature
# Output
outputName $outputname
restartfreq 1000 ;# 500steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 200
outputPressure 200
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#############################################################
## EXECUTION SCRIPT ##
#############################################################
#For heating, use temperature reassignment
reassignFreq 2
reassignTemp 10
reassignIncr 0.01
reassignHold 60
# Minimization
#minimize 10000
#reinitvels $temperature
reinitvels $temperature
run 10000 ;#
Thank you all for your help!
Jack
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