[gmx-users] how to repeat simulation correctly?

Felipe Pineda, PhD luis.pinedadecastro at lnu.se
Thu Nov 22 09:52:08 CET 2012

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?


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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