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

[Berk Hess]

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?
>>>
>>>
>>>>>
>>>>> 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.
>>>
>>>
>>
>
>