AMBER Archive (2006)

Subject: RE: AMBER: ntt=1 in simulated annealing

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Nov 03 2006 - 20:04:08 CST

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

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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Tanya Johannsen
Sent: Friday, November 03, 2006 16:39
To: amber_at_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/section
5.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_at_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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