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

Berk Hess hess at kth.se
Sun Jun 7 23:23:46 CEST 2015 

On 06/07/2015 11:16 PM, David van der Spoel wrote:
> On 07/06/15 23:06, Berk Hess wrote:
>> On 06/07/2015 11:00 PM, David van der Spoel wrote:
>>> On 07/06/15 21:51, Peter Ahlström wrote:
>>>> Hello,
>>>> I've been following the discussion for a while and came just to think
>>>> about another problem:
>>>> What about the PME - isn't that messing up the energy conservation?
>>>> I believe that that's also a non-conservative force -or am I 
>>>> completely
>>>> wrong?
>>>
>>> It computes just the Coulomb energy (or Lennard Jones dispersion) in a
>>> complex way. We tried to turn off the Lennard Jones PME (using a
>>> cutoff) and that leads to poorer energy conservation. One can in fact
>>> control the error in the algorithm to be very small, so I think it is
>>> not a source of error. The known disadvantage of PME is of course that
>>> it enhances periodicity.
>> PME conserves energy perfectly (apart from the cut-off effect which you
>> control with ewald_rtol), so that's not an issue.
>>
>> Thermostats are tricky for energy conservation, since they mess with the
>> velocities. NH with a short period is bad, since the fast oscillations
>> need a short time step for accuracy. Any thermostat with a long period
>> can cause issues, because the velocity scaling factor only differs from
>> 1 by the last few bits, thereby causing systematic rounding errors.
>> Using LF or VV does not influence these issues much.
>> If I need a thermostat and reasonably good energy conservation I use
>> v-rescale with a not too short period and a longer nsttcouple to avoid
>> systematic bit rounding.
>>
>> But why do you want "perfect" energy conservation with NVT? You usually
>> want that with NVE.
>
> We need good energy conservation in order to compute heat capacities 
> from fluctuations. Of course one can do tricks like subtracting the 
> drift or doing simulations at multiple temperatures, but that is 
> sticking your head in the sand.
>
> It seems that double precision works much better than single. If your 
> observation about the problem being x_n+1 = x_n + v_n dt is correct it 
> means we may need to store x in double to be able to do this.
Probably. I think this is the dominant source of error (but I hope my 
student starts analyzing this).
Note that also making v double precision should add negligible overhead.
>
> Or would a unit change to pm and fs help? It seems too simple to be true.
No.
>
> We need NVT because we want to compare our results to experimental 
> data at 298.15K, not at 298.15 +/- 20K.
Then you just need to use a bigger system.

Berk
>
>>
>> Berk
>>
>>>
>>>> Cheers,
>>>> Peter
>>>>
>>>>
>>>>
>>>> Dr Peter Ahlström
>>>> University of Borås
>>>> SE-501 90 Borås
>>>> Sweden
>>>> +46 33 435 4675
>>>>
>>>>  >>> David van der Spoel <spoel at xray.bmc.uu.se> 06/07/15 5:58 PM >>>
>>>> On 02/06/15 13:45, Shirts, Michael R. (mrs5pt) wrote:
>>>>  >> How do we run more NVE than with the settings below?
>>>>  >
>>>>  > tcoupl = Nose-Hoover
>>>>  >
>>>>  >
>>>>  > Would make it not NVE.
>>>>  >
>>>>  > Do you mean the conserved quantity isn't conserved? Energy 
>>>> certainly
>>>>  > won't be conserved with Nose-Hoover.
>>>> Disturbing altogether.
>>>>
>>>> Is there any reason that md-vv would be better than the md integrator
>>>> for energy conservation?
>>>>
>>>>  >
>>>>  > 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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>>>
>>>
>>
>
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