AMBER Archive (2008)

Subject: RE: AMBER: Non bond list error

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Oct 23 2008 - 13:38:09 CDT

Hi Wang,

800K atoms is pretty large and while sander / pmemd should support this size
(I think 999,999 is the limit right now due to file formatting) you may run
into problems that haven't been seen before.

It's not obvious what is going wrong in your case but the numbers don't make
any sense (a negative capacity!) which suggests either memory corruption
through an array overflow or the number of pairs is larger than a signed
integer and is overflowing. Even at 800K atoms you shouldn't have this many
pairs though. Can you post your input file so we can take a look? I suspect
you have cut set too high or perhaps are not running PME etc.

All the best
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Wang,Ying
> Sent: Thursday, October 23, 2008 10:20 AM
> To: amber_at_scripps.edu
> Subject: AMBER: Non bond list error
>
> Hi, Dear AMBERs,
>
> I meet a problem when I run a simulation of a system consist of
> 799889 atoms.
>
> * NB pairs 451 0 exceeds capacity (
> -28510921) 7
> SIZE OF NONBOND LIST = -28510921
> SANDER BOMB in subroutine nonbond_list
> Non bond list overflow!
> check MAXPR in locmem.f
>
> Could anyone tell me what's happen?
>
> Thanks a lot!
>
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