Problem in energy conservation in NVE ensemble with 1fs timestep

From: tinni sona (
Date: Thu Aug 14 2008 - 11:27:18 CDT

Hi All,

I'm doing a NVE simulation in NAMD using AMBER force field. I used
input coordinate and velocity files from a NVT simulation which was
equilibrated at desired temperature (300 K). Looking at TOTAL it is
seen that my system's energy underwent a slow linear
drift (from -87435.3852 to 8115.9629 in 200 ps ). The TEMP of the
system is also fluctuating in the range 295K to 304K.

The .conf file I used is given below:

# NAMD configuration file for CD44_HA (NVE) EQUILIBRATION

firsttimestep 6100000

# input file
set input CD44_HA_equilibration30
coordinates CD44_HA_minimization_restart_f.pdb
bincoordinates $input.restart.coor
binvelocities $input.restart.vel

# output file
set output CD44_HA_equilibration31
outputName $output
restartName $output.restart
binaryoutput yes
binaryrestart yes

cellBasisVector1 70.263 0.0 0.0
cellBasisVector2 0.0 70.263 0.0
cellBasisVector3 0.0 0.0 70.263
wrapWater on
wrapAll on

# force field
amber on
parmfile CD44_HA_ff99SB.prmtop
exclude scaled1-4
1-4scaling 0.833333

# approximations
switching off
cutoff 12
pairlistdist 13.5
margin 0

timestep 1.0
rigidBonds all
rigidTolerance 0.0005
nonbondedFreq 1
fullElectFrequency 1
stepspercycle 10

#PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 72
PMEGridSizeY 72
PMEGridSizeZ 72

restartfreq 1000 ;# 500steps = every 1ps
dcdfreq 500
xstFreq 1000
outputEnergies 1000
outputPressure 1000

langevinPiston off

run 200000

I will highly be oblised if someone can give me an advice about how to
get my simulations conservative. Please help.


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