Ah, I tried reducing the 2.5 to a smaller number before... I must have
forgotten to recompile then. Sorry for my mistake. With a proper
recompile, this remedies the problem. Thanks!
The reason I was not using pmemd was because it crashed with the error:
fill_bonded: max14 exceeded!!
And the patch that was suggested to fix this error previously was for
an earlier version of sander. Can a sander patch be applied to pmemd?
I am not at all familiar with the code and was not sure of what I
might break by trying something like this... The sander patch was
suggested here: http://dev-archive.ambermd.org/200811/0021.html
On 11/25/09, case <case.biomaps.rutgers.edu> wrote:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 25 2009 - 11:00:02 PST
