[gmx-developers] Conserved energy drifts more with shorter time steps
Berk Hess
hess at kth.se
Tue Jun 2 15:25:44 CEST 2015
On 2015-06-02 15:20, Anton Feenstra wrote:
> On 02-06-15 15:14, Berk Hess wrote:
>> On 2015-06-02 15:08, David van der Spoel wrote:
>>> 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?
>> I explained that before, see 4 steps above.
>>
>> Berk
>>>
>>>
>>>>
>>>> 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?
>
>
> Yes, at least that is what I saw for my and Berk's 1999 JCC paper.
> At single precision, drift would not go down below a certain time
> step. I have no idea anymore which timestep precisely, and I'm sure
> this would be system specific.
>
> I also recall drift indeed going up at (extreme) short timesteps. My
> intuition for that at the time was that arithmetic errors would
> accumulate faster for calculating many very small delta's.
In that case it was due to the constraint algorithms. The velocity was
corrected with the coordinate difference divided by the time step. Thus
bit noise is amplified inversely proportional with the time step. I
fixed this some years ago for LINCS and SHAKE, but SETTLE still has this
property.
David is not using constraints. So I think the issue here is, as I
mailed before, that the pairlist buffer estimate is more less accurate,
more of an overestimate, for longer pairlist lifetimes (larger time
steps with fixed nslist), which leads to less drift.
Berk
>
>
>>>>>
>>>>>
>>>>>>>
>>>>>>> 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.
>>>>>
>>>>>
>>>>
>>>
>>>
>>
>
>
More information about the gromacs.org_gmx-developers
mailing list