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

[David van der Spoel]

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
>>
>> * 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.
>


-- 
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