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

[Shirts, Michael R. (mrs5pt)]

> 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.

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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