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

Sun Jun 7 23:06:30 CEST 2015

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.

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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