From: Leonardo Sepulveda Durán (leonardosepulveda_at_gmail.com)
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 cycle...so 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.
Thanks
Leonardo
PD: I attach a .pdf with temperature and energy from my simulation.
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