Re: [AMBER] Query regarding NVT ensemble with less restraint on solute

From: Hirdesh Kumar <>
Date: Sat, 29 Jan 2011 23:25:43 +0530

Thanks Sangita and Jason for your comments. Just another thing.. Recently I
read a research paper in which the author did the NVT heating step, followed
by long NPT equilibration and again NVT run before going to actual
production. I am curious to know why one should proceed to NVT ensemble
after NPT equilibration in any circumstances.


On Sat, Jan 29, 2011 at 7:51 PM, case <> wrote:

> On Sat, Jan 29, 2011, Hirdesh Kumar wrote:
> > I heated my system (protein of 329 residues) gradually over a period of
> > ,000 steps using ntt=3 and gamma_ln = 1.0, with a weak restraint on the
> > solute (i.e. 5 kcal/mol). Is there any need to remove the restraint
> slowly
> > using NVT ensemble further or I should directly proceed to NPT ( without
> any
> > restraint on solute) ensemble as the restraint applied during heating was
> > very slow.
> I would recommend keeing the restraints on during NPT. After you have a
> good
> density, I often run a further equilibration run with 0.5 kcal/mol-A^2
> restraints, but that may just be habit...I haven't with/without tests.
> After that you should run yet more equilibration with no restraints, before
> starting an "production" runs. Don't skimp on equilibration: it can take
> many, many nanoseconds for a big protein to adjust to the force field.
> ....dac
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Received on Sat Jan 29 2011 - 10:00:02 PST
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