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

From: Carlos Simmerling <>
Date: Thu, 22 Mar 2007 17:30:05 -0400

yes it is, make sure you have applied all of the bugfixes.

On 3/22/07, Hu, Shaowen (JSC-SK)[USRA] <> wrote:
> Hi Dr. Case,
> Is this possible to use ntt=3 for simulation annealing? It seems that
> all people use ntt=1 for SA.
> Thanks,
> Shaowen
> -----Original Message-----
> From: [] On Behalf
> Of David A. Case
> Sent: Wednesday, March 21, 2007 2:30 PM
> To:
> Subject: Re: AMBER: ntt=1 or ntt= 3?
> 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
> here:
> %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.
> ...dac
> -----------------------------------------
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Received on Sun Mar 25 2007 - 06:07:30 PDT
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