[gmx-developers] Conserved energy drifts more with shorter time steps
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jun 2 15:08:13 CEST 2015
On 02/06/15 14:30, Berk Hess wrote:
> 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.
Ok, will try. What about the time step dependence? Any clue?
>
> 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
>>>>> --
>>>>> Gromacs Developers mailing list
>>>>>
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List
>>>>> before
>>>>> posting!
>>>>>
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>> * For (un)subscribe requests visit
>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
>>>>>
>>>>> or send a mail to gmx-developers-request at gromacs.org.
>>>>
>>>> --
>>>> Gromacs Developers mailing list
>>>>
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List
>>>> before posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
>>>> or send a mail to gmx-developers-request at gromacs.org.
>>
>>
>
--
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
More information about the gromacs.org_gmx-developers
mailing list