From: Radak, Brian K (bradak_at_anl.gov)
Date: Fri Jun 02 2017 - 10:10:01 CDT
Are you using Langevin dynamics? Center of mass momentum should only be conserved during Newtonian dynamics (maybe also with a deterministic thermostat like Berendsen).
I'm also not sure that zeroMomentum guarantees that the center of mass itself is stationary.
Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
brian.radak_at_anl.gov
________________________________
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of M. Wong [mckwxp_at_gmail.com]
Sent: Friday, June 02, 2017 4:10 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Center of mass drift
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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