Re: AMBER: ntt=1 or ntt= 3?

From: David A. Case <>
Date: Wed, 21 Mar 2007 12:29:45 -0700

On Wed, Mar 21, 2007, Therese Malliavin wrote:
> 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.

I think we need more information. I've equilibrated many systems using ntt=3
and gotten correct densities. So, I don't think there is anything
intrinsically wrong with that option. You could equilibrate with ntt=1,
getting a proper density, then continue with ntt=3, and the temperature and
density should continue to be appropriate.

> 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).

This part sounds correct: if the density is too low, the pressure should be
negative (saying that the system wants to contract). But it's not clear why
the system doesn't contract, leading to a higher density. What value of taup
and ntp are you using? How long was the equilibration? Did you "start over"
in equilibration, or continue an existing run where ntt=1 had been used?

Prof. Duan is correct in saying that ntt=1 with a value of tautp of 1 or 2
doesn't show obvious problems (for explicit solvent simulations). I'm not
sure what he means by saying "for some reason, tautp=0.2 remained on the
manual." (I don't see that myself: the default value is 1.0). The use of
ntt=1 can become problematic for implicit solvent simulations, where there are
relatively few degrees of freedom. And, the Berendsen algorithm is fragile,
and can lead to a non-uniform distribution of temperature inside a simulation
even when the overall temperature looks OK.

On the other hand, Langevin (ntt=3) simulations can also exhibit funny
behavior, especially if the same random number seed is used for repeated
simulations. This problem has a long history, but a good recent overview is

%A B.P. Uberuaga
%A M. Anghel
%A A.F. Voter
%T Synchronization of trajectories in canonical molecular-dynamics
simulations: Observation, explanation, and exploitation
%J J. Chem. Phys.
%V 120
%P 6363-6374
%D 2004

A recommendation is that you should explicitly set the random number seed
("ig") to new values at each restart of an ntt=3 simulation.

The bottom line is that all methods of constant T simulation have
idiosyncracies (including Nose-Hoover thermostats, not discussed here), and
one needs to take care. But the massive problems reported by Therese probably
have some other origin.


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Received on Sun Mar 25 2007 - 06:07:16 PDT
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