RE: AMBER: Amber 8 - Energy Minimization Parameters

From: Ross Walker <>
Date: Wed, 25 Aug 2004 09:02:31 -0700

Hi Hang,

> In the manual (p. 102) the default for MAXCYC is 1. Does it
> mean that if
> I set it at 1, the system will keep running until it reaches the
> closet local minimum?

No, it means the program will do a single step of minimisation and quit. I.e
it will simply calculate the energy of the current configuration. It will
not actually do any minimisation.

> Does this also mean that one has no control nor
> prediction over how long this minimizing process will go?

To do what you mentioned above you would just set Maxcyc to some very high
number - like 100,000. In this case, yes, you would have to either wait
until 100,000 steps had elapsed or the RMS had decreased below the
convergence criteria. Note, the steepest descent method will not normally
get you down much below 10^-2. Conjugate gradient will get you further but
you probably won't ever get to very very tight convergence like you could
with a second derivative method.

The purpose of minimisation in sander is normally just to remove the largest
strains before MD so typically you would not need to get very close to a
minimimum. Thus you would typically set maxcyc to something like 2,500. That
way the minimisation will halt after 2,500 steps. If you need to minimise
further at this point you can just repeat the minimisation using the
previous restrt file as the starting structure.

> Another related issue is that: in the tutorial (DNA - an excellent
> tutoria!), the suggested, trial value for MAXCYC is 500.
> This allows the
> program to perform 500 nstep (which I guess corresponds to
> some number of
> cycles); and the program stops when it reaches the nstep of
> 500. Is this
> value contradicted with the default value of 1?

The reason for the minimisation in the tutorial was simply to allow the
system to relax from the "artificial" hydrogenation before running MD.
Failing to minimise here would probably have led to very large initial
forces and hence velocities which could have led to the system "blowing up".
Typically you should make an estimate at how many minimisation steps to run.
The bigger your system the more degrees of freedom so the more steps you
need. Running too many steps before MD won't do you any harm, it will just
waste cpu time.

I hope this helps.
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Thu Sep 02 2004 - 01:15:10 PDT
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