AMBER Archive (2005)

Subject: Re: AMBER: Minimization of avg structure-SANDER Bomb

From: David A. Case (case_at_scripps.edu)
Date: Thu Mar 17 2005 - 10:51:59 CST


On Thu, Mar 17, 2005, Vineet Pande wrote:
>
> * NB pairs 394 11607260 exceeds capacity ( 11607624) 0
> SIZE OF NONBOND LIST = 11607624
> SANDER BOMB in subroutine nonbond_list

> MY INPUT IS:
> Total minimization
> &cntrl
> ntf = 1, ntb = 2, dielc = 1,
> cut = 8.0, nsnb = 25,
> imin = 1, maxcyc =15000, ncyc = 2500,
> ntmin = 1, dx0 = 0.1, drms = 0.01,
> ntp = 1, npscal = 1, ntc = 1,
> &end

Minimization doesn't know anything about constant pressure, but that *might*
be messing up an internal size calculation. See if running this a constant
volume will help. This is just a guess, but it seems worth a try, since
we have certainly never tested the combination ntp=1 and imin=1. Does the
error happen right at the beginning, or after some number of steps of
minimization? (Set ntpr=1 to see more details of what is going on.)

...good luck....dac

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