Hi Shaowen,
do a google search for
langevin simulated-annealing amber
since we've talked about this before, and this way you'll see the whole
previous discussion. if that doesn't help, then let us know.
carlos
On 3/22/07, Hu, Shaowen (JSC-SK)[USRA] <Shaowen.Hu-1.nasa.gov> wrote:
> Thanks Carlos. Could you give a range of gamma_ln? I can not find any
> example at hand. As I understand, short gamma_ln means tight coupling,
> right?
>
> Thanks,
> Shaowen
>
> -----Original Message-----
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of Carlos Simmerling
> Sent: Thursday, March 22, 2007 4:30 PM
> To: amber.scripps.edu
> Subject: Re: AMBER: ntt=1 or ntt= 3?
>
> yes it is, make sure you have applied all of the bugfixes.
>
> On 3/22/07, Hu, Shaowen (JSC-SK)[USRA] <Shaowen.Hu-1.nasa.gov> 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: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On
> > Behalf Of David A. Case
> > Sent: Wednesday, March 21, 2007 2:30 PM
> > To: amber.scripps.edu
> > 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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--
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115
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Received on Sun Mar 25 2007 - 06:07:31 PDT
