[gmx-users] Experimental to Simulation Time Period Conversion

[Justin Lemkul]

On 2/12/20 8:23 AM, Peter Mawanga wrote:
> Thanks a lot sir for your reply.
>
> Since experiments take place over hours but the simulations can at best
> approach millisecond levels. I was wondering if there is an acceptable time
> conversion factor from experiments to simulations. For example, the
> simulation data generated over a 350 ns period can be taken as an
> acceptable representation of a 24 hours long experiment.

No, I think there is no justification for such a statement. The time 
scales are entirely different.

Simulations can only address questions within the accessible time 
regime. Enhanced sampling methods may help you better sample states that 
would only be otherwise observed via impractically long simulations, but 
you often lose the kinetic argument in favor of thermodynamics (i.e. you 
can describe the ensemble but not the time taken to interconvert between 
different states).

-Justin

> On Wed, Feb 12, 2020 at 12:52 PM John Whittaker <
> johnwhittake at zedat.fu-berlin.de> wrote:
>
>>> Dear group members
>>>
>>> My sincere apologies for the non-Gromacs related question, but I require
>>> this information urgently and hence posted my query here.
>>>
>>> Could someone please provide me with any guidelines to appropriately
>> model
>>> experimental processes with molecular dynamics simulations?
>> What experimental processes are you talking about? Most timescales of
>> interest for physical processes range from picoseconds to seconds to
>> thousands of years. As you note, most timescales are out of reach of MD
>> (simulating anything interesting over the microsecond timescale is
>> extremely difficult).
>>
>>> Since the simulation periods are usually much shorter than the
>>> experimental
>>> time scales, I was searching for a generally acceptable time reduction
>>> factor or some literature towards that direction.
>> What do you mean by "time reduction factor"? What exactly are you doing?
>> There are enhanced sampling methods which sort of "accelerate" the pace of
>> the process/system you are studying... Perhaps looking in that direction
>> might give you some ideas.
>>
>> Best,
>>
>> John
>>
>>> Any information or suggestion would be greatly appreciated.
>>>
>>> --
>>> Cheers
>>> Peter
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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