[gmx-users] how to repeat simulation correctly?

[Mark Abraham]

On Thu, Nov 22, 2012 at 10:13 AM, Felipe Pineda, PhD <
luis.pinedadecastro at lnu.se> wrote:

> Would "non-deterministic" be correct to characterize the nature of MD as
> well? There is also deterministic chaos ...


An MD simulation is normally deterministic, inasmuch as the inputs and
algorithm determine the output, even if the model physics being simulated
is not determinstic (e.g. stochastic elements to the integration). One
needs to be clear about which aspect is of interest. The simulation is
often not reproducible, either, because of run-time effects like dynamic
load balancing or differences in hardware/compilers/libraries.


> And what about the outcome of starting several trajectories from the same
> equilibrated frame as continuation runs, i.e., using its velocities? Could
> they be considered independent and used to extract that valuable statistics
> mentioned in a previous posting?


Of course, sampling a coloured ball from a bag of balls, putting it back in
without letting go, and taking it back out doesn't create a new sample from
the bag. If all the balls were slowly changing colour and you were trying
to sample the distribution of colours, then that in-and-out process might
be a way to create a new sample, but it depends on the timescales
involved...

So yes, you could start from the same set of positions and velocities and
rely on run-time irreproducibility to introduce differences, and chaos to
amplify those over simulation time, in order to reach points from which you
could make statistically independent simulations. Empirically, you'll need
less simulation time to reach that point if you take active steps to make a
significant difference, like changing the velocity of every atom. You need
to re-equilibrate each time you perturb, but that's generally cheaper than
the alternatives.

Mark


>
>
> Felipe
>
>
> On 11/22/2012 10:04 AM, Erik Marklund wrote:
>
>> Stochastic and chaotic are not identical. Chaotic means that differences
>> in the initial state will grow exponentially over time.
>>
>> Erik
>>
>> 22 nov 2012 kl. 09.52 skrev Felipe Pineda, PhD:
>>
>>  Won't this same stochastic nature of MD provide for different,
>>> independent trajectories even if restarted from a previous, equilibrated
>>> frame even without resetting velocities, i.e., as a continuation run using
>>> the velocities recorded in the gro file of the selected snapshot?
>>>
>>> Felipe
>>>
>>> On 11/22/2012 12:55 AM, Mark Abraham wrote:
>>>
>>>> Generating velocities from a new random seed is normally regarded as
>>>> good
>>>> enough. By the time you equilibrate, the chaotic nature of MD starts to
>>>> work for you.
>>>>
>>>> Mark
>>>> On Nov 21, 2012 1:04 PM, "Felipe Pineda, PhD" <
>>>> luis.pinedadecastro at lnu.se>
>>>> wrote:
>>>>
>>>>  So how would you repeat the (let be it converged) simulation from
>>>>> different starting conditions in order to add that valuable statistics
>>>>> you
>>>>> mention?
>>>>>
>>>>> I think this was Albert's question
>>>>>
>>>>> Felipe
>>>>>
>>>>> On 11/21/2012 12:41 PM, Mark Abraham wrote:
>>>>>
>>>>>  If a simulation ensemble doesn't converge reliably over a given time
>>>>>> scale,
>>>>>> then it's not converged over that time scale. Repeating it from
>>>>>> different
>>>>>> starting conditions still adds valuable statistics, but can't be a
>>>>>> replicate. Independent replicated observations of the same phenomenon
>>>>>> allow
>>>>>> you to assess how likely it is that your set of observations reflect
>>>>>> the
>>>>>> underlying phenomenon. The problem in sampling-dependent MD is
>>>>>> usually in
>>>>>> making an observation (equating a converged simulation with an
>>>>>> observation).
>>>>>>
>>>>>> Mark
>>>>>>
>>>>>> On Wed, Nov 21, 2012 at 8:12 AM, Albert <mailmd2011 at gmail.com> wrote:
>>>>>>
>>>>>>   hello:
>>>>>>
>>>>>>>     I am quite confused on how to repeat our MD in Gromacs. If we
>>>>>>> started
>>>>>>> from the same equilibrated .gro file with "gen_vel        = no" in
>>>>>>> md.mdp,
>>>>>>> we may get "exactly" the same results which cannot be treated as
>>>>>>> reasonable
>>>>>>> repeated running. However, if we use "gen_vel=yes" for each round of
>>>>>>> running, sometimes our simulation may not converged at our simulated
>>>>>>> time
>>>>>>> scale and we may get two results with large differences.
>>>>>>>
>>>>>>>     So I am just wondering how to perform repeated MD in Gromacs in a
>>>>>>> correct way so that our results can be acceptably repeated?
>>>>>>>
>>>>>>> thank you very much.
>>>>>>> Albert
>>>>>>> --
>>>>>>>
>>>>>> --
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>> ------------------------------**-----------------
>> Erik Marklund, PhD
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,    75124 Uppsala, Sweden
>> phone:    +46 18 471 6688        fax: +46 18 511 755
>> erikm at xray.bmc.uu.se
>> http://www2.icm.uu.se/molbio/**elflab/index.html<http://www2.icm.uu.se/molbio/elflab/index.html>
>>
>>
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