AMBER Archive (2009)

Subject: [AMBER] check MAXPR in locmem.f error on minimization

From: Jodi Hadden (jodih_at_uga.edu)
Date: Tue Nov 24 2009 - 17:46:03 CST

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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