[gmx-users] how to repeat simulation correctly?

Erik Marklund erikm at xray.bmc.uu.se
Thu Nov 22 10:04:20 CET 2012

Stochastic and chaotic are not identical. Chaotic means that differences in the initial state will grow exponentially over time.


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

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