Complete error msg as follows
***** System must be very inhomogeneous.
***** Readjusting recip sizes.
In this slab, Atoms found: 119297 Allocated: 91707
* NB pairs 216 21628899 exceeds capacity ( 21629083) 3
SIZE OF NONBOND LIST = 21629083
SANDER BOMB in subroutine nonbond_list
Non bond list overflow!
check MAXPR in locmem.f
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
***** Processor 3
***** System must be very inhomogeneous.
***** Readjusting recip sizes.
In this slab, Atoms found: 119297 Allocated: 91707
* NB pairs 216 21628899 exceeds capacity ( 21629083) 3
SIZE OF NONBOND LIST = 21629083
SANDER BOMB in subroutine nonbond_list
Non bond list overflow!
check MAXPR in locmem.f
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
On Fri, Jun 21, 2013 at 11:36 PM, Chinthaka Ratnaweera <cnr88.msstate.edu>wrote:
> Hi
>
> I am evaluating the stability of a protein-rna complex in ethanol-water
> mixture. I used the packmol program to randomly add ethanol to the box
> containing water. To mimic 0.5 % EtOH concentration I added 148 Ethanols to
> a box containing 77895 water molecules. I was able to minimize the system,
> but the problem is it complains with MD. Both PMEMD.CUDA and Sander.MPI
> failed. Sander complains that "System must be very inhomogeneous". So to
> run MD in parallel versions should the system be homogeneous? Is there a
> way that I can improve homogeneity?
> Thank You
>
> --
> Chinthaka Nadun Ratnaweera
> Mississippi State University
> 310 Presidents Circle
> Starkville, MS 39762
>
--
Chinthaka Nadun Ratnaweera
Hand Lab Rm 1126
Mississippi State University
310 Presidents Circle
Starkville, MS 39762
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Received on Fri Jun 21 2013 - 23:00:03 PDT
