AMBER Archive (2007)

Subject: RE: AMBER: ntt=1 or ntt= 3?

From: Yong Duan (duan_at_ucdavis.edu)
Date: Wed Mar 21 2007 - 12:00:56 CST

I've been using ntt=1 throughout (almost) my whole life (it was ntt=5). For
some reason, tautp=0.2 remained on the manual. Please use a bit longer one
(2.0-10.0). The algorithm is an approximation, as are typical cases in many
practical solutions, works only under WEAK coupling (for strong coupling,
higher order expansion should be used). I've never had any problems,
although many of my friends swear that they have enormous problems with
ntt=1 (guess I have been extremely lucky). Remove the COM motion, though, as
you should.

yong

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Therese Malliavin
Sent: Wednesday, March 21, 2007 10:32 AM
To: amber_at_scripps.edu
Subject: AMBER: ntt=1 or ntt= 3?

Dear AMBER users,

I have a couple of questions about the parameters ntt. I have seen that
several questions have been asked in the past, for versions 7 and 8 of
AMBER, but there are some changes in the documentation of AMBER9, and I
have some trouble with them. So I apologize if the question was already
asked for AMBER 9 (I checked on the archive of the mailing list and did
not find anything).

In documentation of AMBER 8, one finds that ntt=1 and tautp=0.2 are
proposed for the example (p. 103) of usual MD in the NTP ensemble.

In documentation of AMBE 9, the user is told not to use ntt=1: "Unless
you are sure you know what you are doing, please don't use ntt=1!" (p.
103) , and ntt=3 and gamma_ln=1.0 are proposed in the example (p. 96)
for usual MD in the NTP ensemble.

So, I decided to switch from ntt=1 to ntt=3 for running an usual MD
simulation in the NTP ensemble (without QMMM). Before that, I was
heating the system using ntt=1 and a constant volume ensemble.

But, the equilibration simulation has a problem with the water density
which is about 0.84 in place of slightly larger than 1. Also, the
pressure is switched to negative values (mean pressure calculated over
20 ps is about -100 atm, whereas I always found it around 0 in the past
when I was using ntt=1).

So, I would greatly appreciate to have some explanation about the setup
of thermostats in AMBER 9, and about the input values recommended for
the different uses of sander.

Best regards,

Thérèse Malliavin
CNRS research fellow
Unité de Bioinformatique Structurale
Institut Pasteur de Paris

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