On Tue, Nov 24, 2009, Jodi Hadden wrote:
>
> I am trying to run a minimization of a solid glucose cluster with
> extra points (lone pairs on the oxygens) in Amber 11.
>
> On 2 cpus, the minimization runs for 1500 steps and then dies with the
> following error:
>
>
> * NB pairs 248 161448 exceeds capacity ( 161500) 0
> SIZE OF NONBOND LIST = 161500
> SANDER BOMB in subroutine nonbond_list
> Non bond list overflow!
> check MAXPR in locmem.f
>
> I have tried the suggestion by Ross Walker to change the locmem.f line
> maxpr_float = natom * (cutoffnb + skinnb)**3 / 3.0d0
> to
> maxpr_float = max(natom * (cutoffnb + skinnb)**3 / 3.0d0,500000)
> and recompile, but I still get the same error.
That is because that line of code is only executed when numextra == 0, which
is not true for your case. Try modifying the assignment to maxpr_float two
lines below that.
>
> The suggestion by Dave Case to change
> maxpr_float = natom * (cutoffnb + skinnb)**3 / 3.0d0
> to
> maxpr_float = natom * (cutoffnb + skinnb)**3 / 2.5d0
> was already implemented in the current version of Amber and so was unnecessary.
Make the 2.5 value even smaller; sander is trying to estimate the number of
nonbonded interactions, but the estimates may not be valid for solid
glucose with lots of extra points.
Is there a reason you are not using pmemd?
....dac
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Received on Wed Nov 25 2009 - 06:00:04 PST
