Hi Ross,
thanks a lot for your simulation "receipt" and
additional comments !
I was intuitively also thinking about that "change shape" criterion
which is typically actual also in receptor/ligand complexation simulations
as there is (depending on size and flexibility associated systems) obvious
some transformation of kinetic energy to potential one which leads to some
decrease
of temperature if no thermostat is used, but it is question how much such
process
might change temperature which is done mainly by kinetic energy of water
molecules,
and it depends probably on ratio of size of simulated system to size of
the whole simul. box ...
Best wishes,
Marek
Dne Thu, 17 Mar 2011 17:31:23 +0100 Ross Walker <ross.rosswalker.co.uk>
napsal/-a:
> Hi Marek,
>
> So here are my 2 cents on the various ensembles one should use for
> heating,
> equilibration, production etc. This of course comes without a warranty...
>
> It is essential in any explicit solvent simulation to run constant
> pressure
> at some point to equilibrate the density. Whether you continue running
> NPT
> depends on whether you believe your system is likely to change 'shape'
> during a simulation. One of the first things to note is that the
> combination
> most people seem to be using on the list which is NPT (ntb=2,ntp=1 with
> Langevin ntt=3) is about the slowest combination of settings you can use.
> Hence things are always a trade off between getting more sampling or
> using
> 'supposedly' better settings. In my opinion one should typically run the
> following and it is what I do for my simulations.
>
> 1) Heat system using NVT (ntb=1,ntp=0,ntt=3,gamma_ln=1.0)
>
> It is critical to initial heat using NVT because at low temperatures
> the
> calculation of pressure is inaccurate and can cause the barostat to
> overcorrect leading to instabilities. I typically either heat to 100K or
> so
> and then switch to NPT or I run a short (20ps or so) heating stage. The
> key
> is not to run for too long initially in NVT (before NPT) or you will get
> vacuum bubbles form in the solvent.
>
> 2) Equilibrate the system using NPT (ntb=2,ntp=1,ntt=3,gamma_ln=1.0)
>
> Once the system is heated I then continue running Langevin dynamics at
> constant pressure to allow the density to equilibrate. I typically run
> this
> for around 1 to 5ns depending on system size, checking that the density
> converges.
>
> 3) Production using NVT (ntb=1,ntp=0,ntt=1,tautp=10.0).
>
> For production if I don't expect the system to change shape, e.g.
> unfold
> and fold back up etc. then I run NVT but with a very weak Berendsen
> thermostat. The Berendsen thermostat is not good for equilibrating the
> system as it does nothing to ensure that the kinetic energy is
> distributed
> in a Boltzmann distribution, however for an already equilibrated system
> the
> thermostat correction on each step should be minor so this should not
> cause
> an issue. I use a weak coupling (10ps) to approximate NVE. Setting this
> to
> infinite would give you NVE. However, NVE can be tricky to get to work
> well
> when running very long simulations. 2fs with shake is kind of bleeding
> edge
> for NVE, you ideally have to tighten the shake tolerance the PME
> tolerances
> and reduce the time step to get ideal energy conservation (although a
> good
> test to be sure things are working properly). As such while NVT is more
> expensive than NVE it is minor and when you add all the extra tolerances
> needed for NVE, NVT ends up quicker. In my opinion this is a better
> option
> than using langevin for the entire simulation as all of the issues with
> simulation problems, NANs seen on the GPUs etc arise from running long
> ntt=3
> simulations. I would even typically run NPT (if I thought my system would
> change shape) using ntt=1 once the system is equilibrated.
>
> I hope this helps.
> All the best
> Ross
>
>> -----Original Message-----
>> From: Marek Maly [mailto:marek.maly.ujep.cz]
>> Sent: Thursday, March 17, 2011 6:25 AM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] NVT Vs NPT
>>
>> 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
>> >>
>> >
>> >
>> >
>>
>>
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Received on Thu Mar 17 2011 - 10:30:03 PDT
