From: hodak_at_chips.ncsu.edu
Date: Thu Aug 24 2006 - 17:16:03 CDT
Hello,
I am trying to equilibrate my system, I have done over 20 restarts and I
have noticed strange thing: Almost always when I look at RMSD, RMSD
increases at beginning of each restart, while it seems settled for over
the last 10-20% of the run. This way it always seems that after one more
restart RMSD will mostly oscillating, but the next restart brings it
higher (at least initially). I am not sure if this is only coincidence or
if my config file has problem and does not do proper restart or if this is
a namd issue.
I am attaching my config file, please look at it if it looks OK
restart-wise:
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ./full_wb.psf
coordinates ./full_wb.pdb
outputName ./restart25/full_wb_eq_restart25
#set temperature 300
# Continuing a job from the restart files
binCoordinates ./restart24/full_wb_eq_restart24.restart.coor
binVelocities ./restart24/full_wb_eq_restart24.restart.vel
extendedSystem ./restart24/full_wb_eq_restart24.restart.xsc
firsttimestep 72570
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters ../parameters/par_all27_prot_lipid.inp
wrapWater on
wrapAll on
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters
timestep 2.0
rigidBonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
#PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 144
PMEGridSizeY 128
PMEGridSizeZ 128
# Constant Temperature Control
langevin on
langevinDamping 5
langevinTemp 300
langevinHydrogen off
# Constant Pressure Control (variable volume)
useGroupPressure yes
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp 300
#Output
restartfreq 2000
dcdfreq 2000
xstFreq 2000
outputEnergies 500
outputPressure 500
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
#minimize 5000
#reinitvels 300
numsteps 433500
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