From: M. Wong (mckwxp_at_gmail.com)
Date: Fri Jun 02 2017 - 04:10:50 CDT
Dear NAMD users,
I am trying to simulate a water cluster of 1000 water molecules in vacuum
without PBC. I tried COMmotion=no only, as well as COMmotion=no together
with zeroMomentum=yes, but there is still a significant drift of the center
of mass in both cases. Can someone kindly inform me a way to fix the center
of mass?
Thanks in advance,
Marco
P.S. The following is the input file:
amber on
parmfile 1000w.top
ambercoor 1000w.crd
set temperature 300
set outputname eq_1000w_1
firsttimestep 0
temperature $temperature
COMmotion no
zeroMomentum yes
# Force-Field Parameters
exclude 1-3
cutoff 100
switching off
pairlistdist 100
# Integrator Parameters
timestep 1.0
rigidBonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
MSM off
langevinPiston off
# Output
outputName $outputname
restartfreq 100000
dcdfreq 1000
outputEnergies 1000
#############################################################
## EXTRA PARAMETERS ##
#############################################################
sphericalBC on
sphericalBCcenter 0, 0, 0
sphericalBCr1 20
sphericalBCk1 1000
sphericalBCexp1 2
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 1000
reinitvels $temperature
run 100000
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