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

[Berk Hess]

On 2015-06-02 14:26, David van der Spoel wrote:
> 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?
It depends on how low drift you want to be able to measure. You need to 
set it lower than the drift you want to be able to measure.

Berk
>
>> 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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