Hello,
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
On >2 cpus, it dies before any steps are ever made.
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.
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.
I have also tried reducing cutoff to 8.0 as suggested elsewhere, also
to no avail.
Unfortunately, I am not using the absolute newest version of Amber 11.
Does anyone know if this issue has been address in a newer release?
Otherwise, any suggestions?
Thanks much,
Jodi Hadden
Graduate Student
University of Georgia
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Received on Tue Nov 24 2009 - 16:00:02 PST
