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
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
>
>
> --
> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> http://www.opera.com/mail/
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 17 2011 - 09:00:04 PDT
