> * NB pairs 1726 52366155 exceeds capacity ( 52366666)
It is interesting that there are two numbers printed for NB pairs, 1726
and 52366155.
You might try
% grep 'exceeds capacity' *.f
to find where the error is coming from and which variables are
triggering it. I don't have the source these days. It may be something
other than maxpr_float.
Bill
On 2/25/16 2:17 AM, Anna Cebrian Prats wrote:
> Hi,
>
> I am trying to run the minimization with sander
> using a .top file and the inpcrd file as a result of
> using the chamber (executable that convert charmm files to amber files)
> of amber14. The system constitute a large protein with a Fe+2 coordinated with
> 5 residues and a "-OH"
>
> The problem is that I obtain the follow message:
>
>
> --------------------------------------------------------------------------------
>
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
> ---------------------------------------------------
>
> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
>
> using 5000.0 points per unit in tabled values
>
> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
>
> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
>
> | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
>
> ---------------------------------------------------
>
> * NB pairs 1726 52366155 exceeds capacity ( 52366666)
>
> SIZE OF NONBOND LIST = 52366666
>
> SANDER BOMB in subroutine nonbond_list
>
> Non bond list overflow!
>
> check MAXPR in locmem.f
>
>
> I already check MAXPR of the locmen.f and try to modify the assignment
> to maxpr_float two the lines below:
>
>
>>> maxpr_float = natom * (cutoffnb + skinnb)**3 / 2.5d0
>>> to
>>> maxpr_float = natom * (cutoffnb + skinnb)**3 / 1.5d0
>
> and still not working.
>
>
> May I use the pmemd.mpi ? or what I have to check to solve the error?
>
>
> Thank you
>
> Anna
>
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Received on Thu Feb 25 2016 - 03:30:03 PST
