From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Fri Jun 02 2017 - 12:35:12 CDT
Dear Marco,
The zeroMomentum option is intended only for constant energy simulation in order to conserve linear momentum when using either the PME or MSM grid-based long-range electrostatics solvers. It has the benefit of retaining symplecticness of the integrator. Here is a link to the paper for details: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2346486/ <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2346486/>.
As Brian points out, the center of mass is expected to drift when using Langevin dynamics. However, I think a bigger reason for your center of mass drift is due to your spherical restraints, which appears to be a really hard wall tight against your water droplet. Try making the sphere wall further away and much softer. Maybe also monitor outputMomenta to see how changing the spherical restraints affects your simulation.
Best regards,
Dave
-- David J. Hardy, Ph.D. Theoretical and Computational Biophysics Beckman Institute, University of Illinois dhardy_at_ks.uiuc.edu http://www.ks.uiuc.edu/~dhardy/ > On Jun 2, 2017, at 10:10 AM, Radak, Brian K <bradak_at_anl.gov> wrote: > > 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 <mailto: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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