Center of mass drift

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

This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:20 CST