Hi Jason,
which is your opinion on NVE ensamble ?
I think that this question is actual especially in the connection with GPU
calculations due to memory limitations especially in case of GTX .. cards.
According to the information from this web page:
http://ambermd.org/gpus/
(section: "System Size Limits")
NVE ensamble has the smallest memory requirements (and probably the
simulation is fastest here as there is no
time penalty for thermostat, barostat calculations ).
There is just problem that this ensamble in general don't ensure for
constant temperature neither for constant
pressure although if the simulated system is pre-equilibrated using
sufficient NPT (or NPT/NVT) run, probably
changes on P,T during consequent NVE simulation might be so slow
(depending on given solvent and it's concrete model implementation ),
that for sufficient time originally adjusted values of P,T are within the
acceptable tolerance ...
I know that I may do some relevant tests by my self but I am just
wondering if you or someone else already made
such "benchmarks" for example for widely used TIP3P model of water ...
Thanks in advance for comments,
Bets wishes,
Marek
Dne Wed, 16 Mar 2011 17:49:39 +0100 Jason Swails <jason.swails.gmail.com>
napsal/-a:
> Hello,
>
> I'll share my opinion, which may differ from others. NPT is very useful
> for
> equilibrating density, and can relieve artifacts arising due to the fact
> that the system may not have been optimally packed to begin with (which
> is
> the case for tleap-created systems). If you do not run with NPT at all
> (and
> just NVT), then you wind up bubbles appear as the water retracts into its
> *normal* density in the liquid phase.
>
> Thus, during equilibration, NPT is quite useful to maintain a constant
> density and let the box reduce to the "proper" size for the number of
> solvent molecules in your system. However, NPT is more expensive than
> NVT
> because the pressure scaling is not free. Therefore, many people use NVT
> after they've equilibrated at NPT. Solvent (i.e. water) is largely
> incompressible, so NVT and NPT are, for all intents and purposes,
> equivalent
> (for an equilibrated system).
>
> Hope this helps,
> Jason
>
> On Wed, Mar 16, 2011 at 12:31 AM, Mahmoud Soliman
> <mahmoudelkot.gmail.com>wrote:
>
>>
>> Dear guys,
>> I am running MD simulation for an enzyme in a water box. Normally,
>> during
>> heating and equilibration of the system I impose some restraints on
>> some
>> residues and I use NVT during that. But in production, I do not put
>> any
>> restraints and I use NPT. Actually, I learn that from amber tutorials
>> but
>> I
>> see some papers adopting NVT during the production phase... So can you
>> guys
>> provide me with your experience about merits/drawbacks of both
>> protocols
>> (NVT and NPT)...much appreciated!
>> Best wishes
>> Mahmoud
>>
>> --
>>
>> *************************************************
>>
>> Mahmoud E. Soliman
>>
>> Computational Chemistry & Modeling (PhD)
>>
>> Department of Chemistry
>>
>> University of Bath
>>
>> Bath
>>
>> BA2 7AY
>>
>> United Kingdom
>>
>> [1]http://people.bath.ac.uk/mess20/
>>
>> [2]http://www.bath.ac.uk/person/812559
>>
>>
>> *********************************************
>>
>> Mahmoud E. Soliman
>>
>> Lecturer of pharmaceutical organic chemistry
>>
>> Pharmaceutical Organic Chemistry Dept.
>>
>> Faculty of pharmacy
>>
>> Zagazig University
>>
>> Zagazig
>>
>> Egypt
>>
>> **********************************************
>>
>> Email:
>>
>> [3]mess20.bath.ac.uk
>>
>> [4]meelkot.zu.edu.eg
>>
>> [5]mahmoudelkot.gmail.com
>>
>> References
>>
>> 1. http://people.bath.ac.uk/mess20/
>> 2. http://www.bath.ac.uk/person/812559
>> 3. mailto:mess20.bath.ac.uk
>> 4. mailto:meelkot.zu.edu.eg
>> 5. mailto:mahmoudelkot.gmail.com
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
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Received on Thu Mar 17 2011 - 07:00:03 PDT
