RMSD increases after restarts, decreases at the end of run

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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:43:56 CST