How to conservate energy during NVE simulations???

From: Leonardo Sepulveda Durán (
Date: Wed Jun 15 2005 - 20:55:29 CDT

Hello everybody

I was trying to do a NVE simulation in NAMD. I used imput coordinate
and velocity files from a NVT simulation which was equilibrated at
desired temperature (498 K)

Looking at TOTE3, it is obvious my system's energy underwent a slow
drift (from -20235 to -20225 in 250 ps ). The .conf I used is below:

structure ./ubq-wb.psf
coordinates ./ubq-min.coor

# For Continuing a run, otherwise comment all but firsttimestep
set inputname ubq-heat
binCoordinates $inputname.coor ;# coordinates for last run (binary))
binVelocities $inputname.vel ;# velocities for last run (binary)
extendedSystem $inputname.xsc ;# Cell dymentions for last run
firsttimestep 41500 ;# Last step previous run
numsteps 125000 ;# run stops when this
step is reached

# Force-Field Parameters
paraTypeCharmm on
parameters /home/RPMs/NAMD/toppar/par_all22_prot.inp
exclude scaled1-4
1-4scaling 1.0
switching on

switchdist 10.; # cutoff-2
cutoff 12.; # may be 10 with PME
pairlistdist 14.; # cutoff+2
margin 0.498;

# Integrator Parameters
timestep 2.0; # 2fs/step
rigidBonds all; # needed for 2fs steps (SHAKE)
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
outputPairlists 1000

# Periodic Boundary Conditions
cellBasisVector1 50.68 0. 0.
cellBasisVector2 0. 52.37 0.
cellBasisVector3 0. 0. 56.27
cellOrigin 30.85 29.14 17.90

wrapAll on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 54
PMEGridSizeY 54
PMEGridSizeZ 60

# Output
outputName ubq-eq
binaryOutput yes;

restartfreq 500; # 500steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 100
outputPressure 100
outputTiming 1000

I was wondering if someone can give me an advice about how to get my
simulations conservative. I am confused about some concepts and
parameters...for example, in the manual, stepspercycle is explained
as the number of timesteps beetween atom
reasignments; I thought it was refering to pairlist reasignment, but
later "pairlistpercycle" is defined as the number of times pairlists
are regenerated in one if I have

stepspercycle = 20
pairlistpercycle = 2

is the same as using

stepspercycle = 10
pairlistpercycle = 1 ?????

I really dont understand the difference. Also I put outputPairlists
because it sound useful to avoid atoms to pass the pairlist boundary,
but i am not sure if only give the pairlists violations. So I would
like to ask if someone have done NVE simulations succesfully, and what
parameters can be adecuate to do it.



PD: I attach a .pdf with temperature and energy from my simulation.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:40:51 CST