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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Mar 16 2011 - 10:00:04 PDT
