Re: [AMBER] On the usage of the position restrains during equilibration

From: Bill Ross <>
Date: Fri, 20 Jun 2014 08:36:06 -0700

For what it's worth, I thought NVT is preferred for production and NPT to equilibrate volume. Since NVT is faster and less artificial than scaling the box to affect pressure.


-------- Original message --------
From: James Starlight <>
Date:06/20/2014 7:30 AM (GMT-08:00)
To: AMBER Mailing List <>
Subject: [AMBER] On the usage of the position restrains during equilibration

Dear Amber users!

>From the Amber tutorials I've learn that initial heating should be always
done in NVT and production run in any desired ensemble. SupposingĀ  I'm
using NPT for production run performing 100ps NVT pre-equilibration of my
water-soluble system with applied position restrains on all atoms of my
protein. Should I do a short NPT equilibration as well (taking all outputs
from the previous NVT) with the such position restrains applied to the
protein (as I've found in the Gromacs tutorials). What fluctuation to the
system might be introduced by its initial coupling with the Monte Carlo
barostat (for instance seriously deforming protein conformations during
beginning of the NPT phase if pos.res on protein atoms have not been
applied) ?


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Received on Fri Jun 20 2014 - 09:00:02 PDT
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