This may or may not be helpful:
JChemPhys 120(24) 11432-11441 (2004)
This paper states that the optimum gamma is found by integrating the
memory function of an NVE simulation of your system, but as a rule of
thumb the thermostat frequency (= 2*pi / gamma) should be "a few tens of
times smaller than the smallest characteristic frequency of the system
to be studied"
Steve.
Ross Walker wrote:
> Hi Tanya,
>
> The use of such a high gamma_ln in that tutorial has nothing to do with
> the high temperatures it is a function of the way nudged elastic band
> simulations work and the tutorial is specific to this method.
>
> For a regular MD simulation you should not use such a high value of
> gamma_ln. I suspect a value of 1.0 should be perfectly good for your
> simulated annealing. You could perhaps set it a bit higher if you find
> that the system is taking too long to reach the target temperature but
> if all is working fine this is probably okay. One could perhaps argue
> that at higher temperatures the number of collisions that would be
> occuring per ps would be higher and so a higher value of gamma_ln might
> be appropriate but I have no idea of the magnitudes of the changes here.
>
> Perhaps others can comment some more.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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> Note: Electronic Mail is not secure, has no guarantee of delivery, may
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>
>
>
> ------------------------------------------------------------------------
> *From:* owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] *On
> Behalf Of *Tanya Johannsen
> *Sent:* Friday, November 03, 2006 16:39
> *To:* amber.scripps.edu
> *Subject:* Re: AMBER: ntt=1 in simulated annealing
>
> Thank you for your reply. One question: does the use of ntt=3 for
> simulated annealing (and hence high temperatures) affect how I
> should define gamma_ln? Based on tutorials and the literature that
> I've looked at I thought that gamma_ln=1.0 was a pretty reasonable
> choice for room temperature simulations. However, in the only
> tutorial that I've been able to find that uses ntt=3 for simulated
> annealing
> (http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_seven/section5.htm),
> gamma_ln is equal to 1000.0. Does this have something to do with the
> high temperatures? I have consulted the literature and it is not
> clear to me how gamma_ln should be affected (if at all) by
> performing simulated annealing
> rather than a room temperature simulation. I would be very grateful
> if anyone could offer their suggestions on defining gamma_ln.
>
> Thank you in advance.
>
> Tanya
>
>
> */Carlos Simmerling <carlos.csb.sunysb.edu>/* wrote:
>
> you can use the weight changes to make gradual changes to TEMP0
> and it will work fine. Check page 106 of the Amber9 manual and it
> shows you how to do weight changes.
>
> Tanya Johannsen wrote:
>
> > Dear AMBER community:
> >
> > I am working on a simulated annealing run. My understanding
> was that
> > ntt=1 is traditionally used for simulated annealing since it is
> > possible to use the tautp parameter to induce slow and gradual
> > temperature changes. However, I saw that in the AMBER 9 manual
> it says
> > "Unless you are sure you know what you are doing, please don't
> use
> > ntt=1!" If not using ntt=1, what is the best method to use in
> > simulated annealing? My understanding is that ntt=3 leads to a
> > relatively quick adjustment to the target temperature, so even
> if I
> > included many small adjustments in TEMP0, I'm concerned that
> it would
> > be impossible to create a smooth temperature curve. I would
> appreciate
> > any advice on the best choice for "ntt" in simulated annealing
> runs.
> >
> > Thank you in advance for any suggestions.
> >
> > Tanya
> >
> >
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Received on Wed Nov 08 2006 - 06:07:32 PST
