The sander and pmemd codes are completely independent of one another (though
they give the same results for the same simulations). Thus, a patch that
fixes one of the codes will not work on the other (i.e. you cannot apply a
sander patch to pmemd) since the source codes are different.
On Wed, Nov 25, 2009 at 1:29 PM, Jodi Hadden <jodih.uga.edu> wrote:
> 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
> >
> >
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Nov 25 2009 - 11:00:03 PST
