OK, thanks a lot for your comments/suggestions !
Best wishes,
Marek
Dne Thu, 17 Mar 2011 16:49:57 +0100 Jason Swails <jason.swails.gmail.com>
napsal/-a:
> In theory, NVE should give you the same answers, too. You can show that
> all
> thermodynamic ensembles are equivalent (since the fluctuations vanish at
> large particle counts, leaving only the mean terms). However, NVE causes
> some additional problems -- namely you have to be *sure* that you
> conserve
> energy.
>
> If you use a 2 fs time step with a slightly relaxed SHAKE tolerance, you
> can
> be pretty sure that your energy will drift over a fairly small period of
> time. (Run some tests to check this out with just a box of water). If
> NVE
> is done *properly*, the temperature should fluctuate slightly but not
> change
> on average (the fluctuations will go down as particle number goes up). I
> would probably suggest that if your temperature does change appreciably
> over
> a modest test simulation, that you impose a weakly-coupled Berendsen
> thermostat (i.e. pick a very long tautp). Berendsen just works by
> scaling
> velocities, so it should be the fastest option with the smallest memory
> footprint I would expect.
>
> Others may interject here with their opinions.
>
> Hope this helps,
> Jason
>
> 2011/3/17 Marek Maly <marek.maly.ujep.cz>
>
>> 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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>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
>> >
>> >
>>
>>
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Received on Thu Mar 17 2011 - 09:30:02 PDT
