[gmx-users] how to repeat simulation correctly?

[Mark Abraham]

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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>>>
>
> --
> +-----------------------------**------+
> | Luis Felipe Pineda De Castro, PhD |
> | Computational Chemist - Postdoc   |
> | Computational Chemistry and       |
> | Biochemistry Laboratory           |
> | School of Natural Sciences        |
> | Linnaeus University               |
> | SE-391 82 Kalmar                  |
> | Norrgård, room 311                |
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> | E-Mail: luis.pinedadecastro at lnu.se|
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