[gmx-developers] Conserved energy drifts more with shorter time steps
Berk Hess
hess at kth.se
Mon Jun 8 07:47:17 CEST 2015
On 06/08/2015 02:09 AM, Shirts, Michael R. (mrs5pt) wrote:
>> We need good energy conservation in order to compute heat capacities
> >from fluctuations.
>
> But the important thing is not the energy conservation, but how closely
> the simulation matches the Boltzmann ensemble. For example, Langevin
> dynamics does not conserve any energy, but gives the Boltzmann
> distribution exactly. Macroscopically, the heat capacity is defined in
> terms of d<U>/dT, and the fluctuation formula can be derived from this
> derivative definition if the energy distribution is Boltzmann distribution
I wanted to write the same thing.
I was so focused on the (for me very interesting) topic of energy
conservation that I only realized this after posting my last reply. A
run with NH, v-rescale or SD with "moderately" good energy conservation
should suffice.
Berk
>
> This is where I plug checkensemble,
>
> https://github.com/shirtsgroup/checkensemble
>
> Described here:
>
> http://dx.doi.org/10.1021/ct300688p
>
>
> Which shows how one can perform tests to check whether a given set of
> simulation conditions gives the Boltzmann distribution in the output (also
> works for NVT, NPT, etc).
>
> Also, for good estimation of the heat capacities:
>
> https://github.com/choderalab/pymbar/examples/heat-capacity
>
>
> has an example of heat capacity calculated via MBAR in several different
> ways - by fluctuation, by finite difference by perturbed expectation, and
> by second derivative of the free energy.
>
> Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Associate Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434) 243-1821
>
>
>
> On 6/7/15, 5:16 PM, "David van der Spoel" <spoel at xray.bmc.uu.se> 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.
>>
>> Or would a unit change to pm and fs help? It seems too simple to be true.
>>
>> We need NVT because we want to compare our results to experimental data
>> at 298.15K, not at 298.15 +/- 20K.
>>
>>> 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
>>>>> >> --
>>>>> >> Gromacs Developers mailing list
>>>>> >>
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>>>>> >> posting!
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>>>>> >> 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
>>>>> --
>>>>> Gromacs Developers mailing list
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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
>> --
>> Gromacs Developers mailing list
>>
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