Hi Manu
I think the density of your simulation box is increasing so you are
seeing an increase in the number of the nonbonded pairs list and I guess
the program conked when it realized that the number of nonbonded pairs
it needs to handle is larger than what it can.
Heard from DB about your normal modes calculation, sounds interesting.
Best wishes,
Surjit
Emmanuel Giudice wrote:
> Hi
> I'm using amber7 to simulate a protein dna complex( 6593 atoms, 372
> residues) with explicit water (11955 TIP3P) and counter ions (30 K+, 13
> Cl-, 2Mg).
> I have simulated successfully this system on a PC cluster as well as an
> equivalent system (same protocol, same number of atoms and residue, one
> more covalent bond) on a single machine. However this time when I try
> the simulation on my PC, I received an error message about the size of
> the Non bond list. I can increase the parameter MAXPR in size.h and
> recompile but what I don't understand is the difference between the
> total size of non bond list : 11882628 at the beginning, 11999932 at the
> error point, and the error message itself ( for me 11999932 doesn't
> exceeds 12000000).... any explanations will be appreciated
>
> Thanks,
> Manu
>
> PS: these are the last lines of my output file
>
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 11882628
> | TOTAL SIZE OF NONBOND LIST = 11882628
>
> NSTEP = 0 TIME(PS) = 50.000 TEMP(K) = 0.00 PRESS = -1126.2
> Etot = -138323.2656 EKtot = 0.0000 EPtot = -138323.2656
> BOND = 1286.3115 ANGLE = 3218.1226 DIHED = 2494.3721
> 1-4 NB = 1516.2947 1-4 EEL = 9645.0116 VDWAALS = 13131.3806
> EELEC = -169614.7587 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 0.0000 VIRIAL = 10243.0535 VOLUME = 421262.1660
> Density = 1.0460
> Ewald error estimate: 0.1260E-03
> ------------------------------------------------------------------------------
>
>
>
> * NB pairs 294 11999932 exceeds capacity ( 12000000) 0
> SIZE OF NONBOND LIST = 12000000
> EWALD BOMB in subroutine ewald_list
> Non bond list overflow!
> check MAXPR in sizes.h
>
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Received on Thu Feb 26 2004 - 22:53:00 PST
