From: M. Wong (mckwxp_at_gmail.com)
Date: Sat Jun 03 2017 - 04:44:18 CDT
Thanks David and Brian for your valuable suggestions. I tried to use MSM
with my simulation together with zeroMomentum, and then the COM does not
drift anymore.
Best,
Marco
2017-06-03 1:35 GMT+08:00 David Hardy <dhardy_at_ks.uiuc.edu>:
> 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/.
>
> 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
> ------------------------------
> *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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