[gmx-developers] Conserved energy drifts more with shorter time steps

[David van der Spoel]

On 07/06/15 21:51, Peter Ahlström wrote:
> Hello,
> I've been following the discussion for a while and came just to think
> about another problem:
> What about the PME - isn't that messing up the energy conservation?
> I believe that that's also a non-conservative force -or am I completely
> wrong?

It computes just the Coulomb energy (or Lennard Jones dispersion) in a 
complex way. We tried to turn off the Lennard Jones PME (using a cutoff) 
and that leads to poorer energy conservation. One can in fact control 
the error in the algorithm to be very small, so I think it is not a 
source of error. The known disadvantage of PME is of course that it 
enhances periodicity.

> Cheers,
> Peter
>
>
>
> Dr Peter Ahlström
> University of Borås
> SE-501 90 Borås
> Sweden
> +46 33 435 4675
>
>  >>> David van der Spoel <spoel at xray.bmc.uu.se> 06/07/15 5:58 PM >>>
> On 02/06/15 13:45, Shirts, Michael R. (mrs5pt) 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.
> Disturbing altogether.
>
> Is there any reason that md-vv would be better than the md integrator
> for energy conservation?
>
>  >
>  > Best,
>  > ~~~~~~~~~~~~
>  > 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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>
> --
> 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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-- 
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