[gmx-developers] Conserved energy drifts more with shorter time steps
Shirts, Michael R. (mrs5pt)
mrs5pt at eservices.virginia.edu
Tue Jun 2 13:51:22 CEST 2015
> 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.
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
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:
>> 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?
>> On 2015-06-02 12:43, David van der Spoel wrote:
>>> 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
>>> 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?
>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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