Restarting problem with Langevin dynamics

From: Xin Chen (
Date: Wed Mar 31 2004 - 15:11:58 CST

Hi, all

I used Langevin dynamics to control the temperature in the simulation. But
it seems that I cannot restart my simulation with it. First time, I did
simulation to 1.6M timestep, and then I restart it from 1.5M timestep. The
energy results from 1.5M to 1.6M timestep for these two simulation are
different. The force field I used is AMBER. I wonder if anyone know why and
how to solve this problem. Thanks. The configuration files is as follows

First one
numsteps 1600000

# initial config
temperature 373.16
seed 12345
#rigidBonds all
# output params
#cwd ./out0
outputname botulinum_water
binaryoutput no
outputEnergies 500
outputMomenta 0
outputTiming 500
outputPressure 0
# integrator params
timestep 1.0

# force field parameters
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 10.0
cutoff 12.0
pairlistdist 14.0
pairlistsPerCycle 10
margin 4.0
stepspercycle 20

langevin on # langevin dynamics
langevinFile 3bta_wat.pdb
langevinDamping 5.0 # damping coefficient of 5/ps
langevinTemp 373.16 # random noise at this level

maximumMove 0.5

wrapWater on # wrap water to central cell
wrapAll on # wrap other molecules too
wrapNearest off # use for non-rectangular cells

# we are using amber force field

amber yes
ambercoor 3bta_wat.crd
readexclusions no
scnb 1.0

binaryrestart yes
DCDfile bta_wat.dcd
DCDfreq 10000
DCDUnitCell yes
velDCDfile bta_wat.vcd
velDCDfreq 20000

restartname bta_wat
restartfreq 5000
restartsave yes


Second one:

Same, add one line:

firsttimestep 1500000

Sincerely yours,

Xin Chen

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