minimization in amber7 for nonperiodic systems

From: David Case <>
Date: Tue 13 Aug 2002 22:47:43 -0700

Several people have noted recently that some types of minimization in
Amber 7 perform very poorly. Here are things that should help; I
am primarily thinking of non-PME (ntb=0) systems:

(1) If you can at all afford it, use a very large cutoff (e.g. 999.).
Conjugate gradient minimization is very sensitve to cutoffs, and in Amber
(all versions) it is often a poor economy to try to skimp on the cutoff
during minimization. Also, turn off SHAKE (set ntf=ntc=1); you *can* leave
SHAKE on, but only for short minimizations whose purpose is to remove bad
contacts before MD can begin.

(2) If you really cannot use an infinite cutoff, use as large a one as you
can (especially when igb=0), and set nbflag=0, skinnb=0. in the &ewald
namelist. [Notes: yes, this should have been in the Users' Manual; no,
the fact that these variables are in the &ewald namelist does *not* mean
that they are only important for PME simulations, although it is certainly
understandable that a user would think that.]

Setting nbflag=0 makes nsnb (the frequency of nonbonded updates) an
important variable. I haven't done lots of tests, but the default value
of 25 seems reasonable good: you get 25 steps of conjugate gradient before
re-making the non-bonded list, which triggers a "restart" of the conjugate
gradient procedure. But especially with non-periodic systems with water,
there is a real limit to what one can do with minimization using the
current Amber cutoff scheme. But nbflag=0, skinnb=0. *should* get you back
the performance one used to get in earlier versions. Future releases will
make these the default for minimization.

(3) Mike and Tom: the above is another reason why we need to implement
a switching scheme more general than erf/erfc (and/or implement non-periodic

Thanks to those of you that have brought the problem to our attention;
please let us know if items (1) or (2) above don't help.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Tue Aug 13 2002 - 22:47:43 PDT
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