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

From: case <>
Date: Sat, 29 Jan 2011 09:21:27 -0500

On Sat, Jan 29, 2011, Hirdesh Kumar wrote:

> I heated my system (protein of 329 residues) gradually over a period of
> 50,000 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.


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Received on Sat Jan 29 2011 - 06:30:02 PST
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