[gmx-developers] Conserved energy drifts more with shorter time steps
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jun 2 14:26:04 CEST 2015
On 02/06/15 14:05, Berk Hess wrote:
> I assume David is looking at the conserved energy quantity.
Indeed, averages and drift over 900 ps, 1000 molecules:
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Total Energy 20460.7 2.5 778.213 12.4265 (kJ/mol)
Conserved En. -4384.7 380 778.283 2665.29 (kJ/mol)
>
> 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.
>
This may be the default.
verlet-buffer-tolerance = 0.005
should we set it to 1e-5 or something like that?
> 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.
Turning tcoupl off would not keep the temperature constant of course,
seeing that there is a drift in the conserved energy this means that the
temperature will change.
However, the main question was why does "conserved-energy conservation"
get worse when the time step is reduced? Integration should presumably
become more accurate, or not? Or does one need double precision for
short time steps?
>>
>> 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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--
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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