AMBER Archive (2004)

Subject: Re: AMBER: NSNB parameter

From: Robert Duke (
Date: Sat Apr 24 2004 - 22:05:51 CDT

David -
I have not examined the code in excruciating detail, but I think what you
say about minimization is "newly" true for sander 8. In the case of sander
7, the setting of nbflag to turn on fixed pair list updates was commented
out in the code. In sander 6, it was not even there in a comment, and pmemd
minimization behaviour was first modeled on 6. So in pmemd, while I retain
nsnb because it is used rather mysteriously in setting a "steepest descent"
flag (an undocumented behaviour, as far as I know), it has no control over
the frequency of pairlist builds unless you explicitly set nbflag to 0. So,
bottom line, in sander 6 and 7, fixed pairlist builds are not done unless
you make an explicit effort after reading about nbflag in the manual. In
pmemd, by 3.1 and possibly earlier I ignore explicit requests and issue a
warning so you know that I ignored nbflag. I really have not seen any
problems with doing away with fixed pairlist updates entirely. In
minimization, because things don't move much, the pairlist updates are
really infrequent, but with the skincheck they occur when needed.
Regards - Bob
----- Original Message -----
From: "David A. Case" <>
To: <>
Sent: Saturday, April 24, 2004 4:13 PM
Subject: Re: AMBER: NSNB parameter

> On Sat, Apr 24, 2004, Robert Duke wrote:
> > In my opinion, the approach of updating the pair list at fixed intervals
> > outmoded.
> Bob is correct, except that fixed pair list updates are still needed for
> minimization, which is why such code is still there in sander. And
> is set correctly automatically: there is generally no need for a user to
> change the defaults. (An experienced user might occasionally do so for
> debugging...)
> ...dac
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