[gmx-developers] Conserved energy drifts more with shorter time steps
hess at kth.se
Tue Jun 2 14:05:14 CEST 2015
I assume David is looking at the conserved energy quantity.
But I just noticed that Verlet - buffer - tolerance is not mentioned, so I assume it is default. The drift estimate is an overestimate which is tighter for shorter pair list lifetimes. I guess that is the explanation. Set it very low, so you are sure the energy drift is not affected by the (too small) buffer.
On Jun 2, 2015 1:45 PM, "Shirts, Michael R. (mrs5pt)" <mrs5pt at eservices.virginia.edu> wrote:
> > How do we run more NVE than with the settings below?
> tcoupl = Nose-Hoover
> Would make it not NVE.
> Do you mean the conserved quantity isn't conserved? Energy certainly
> won't be conserved with Nose-Hoover.
> Michael Shirts
> Associate Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434) 243-1821
> On 6/2/15, 7:22 AM, "David van der Spoel" <spoel at xray.bmc.uu.se> wrote:
> >On 02/06/15 12:47, Berk Hess wrote:
> >> Hi,
> >> So this is not using SETTLE or LINCS?
> >> With SETTLE this is a known issue.
> >No this is flexible organic molecules at contant volume.
> >> Did you try running NVE?
> >How do we run more NVE than with the settings below?
> >> Cheers,
> >> Berk
> >> On 2015-06-02 12:43, David van der Spoel wrote:
> >>> Hi,
> >>> this is in between a user and a developer query. We find that for
> >>> flexible liquid simulations using gromacs 5.0.4/single precision the
> >>> energy conservation gets WORSE with decreasing time step. A plot
> >>> showing this is in
> >>> http://folding.bmc.uu.se/images/Econserved-timestep.xvg or
> >>> http://folding.bmc.uu.se/images/Econserved-timestep.pdf
> >>> MDP settings
> >>> coulombtype = PME
> >>> coulomb-modifier = Potential-shift
> >>> rcoulomb-switch = 0
> >>> rcoulomb = 1.1
> >>> epsilon-r = 1
> >>> epsilon-rf = inf
> >>> vdw-type = PME
> >>> vdw-modifier = Potential-shift
> >>> rvdw-switch = 0
> >>> rvdw = 1.1
> >>> tcoupl = Nose-Hoover
> >>> nsttcouple = 10
> >>> nh-chain-length = 1
> >>> pcoupl = No
> >>> ref-t: 298.15
> >>> tau-t: 0.5
> >>> Any clues whether we are doing something wrong? Or is there a bug?
> >>> Cheers,
> >David van der Spoel, Ph.D., Professor of Biology
> >Dept. of Cell & Molec. Biol., Uppsala University.
> >Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> >spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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