[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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