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

[Berk Hess]

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.

Berk

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. 
>
> 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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