Dear Carsten,
Please indicate what version of sander you are running.
Can you send more output? It appears that you want to run
a nonperiodic simulation, but it is not clear to me that
you have succeeded. If you had succeeded, and if sander is
working properly, then with a 999999 A cutoff, you should see
(.5)(4600)(4600-1) pairs (all the pairs) which comes out to
10.6 million pairs, not over 100 million pairs.
Please describe (send output) what you did and what you want to do
and we will see if we can find the trouble.
Sincerely,
Mike
-----------------------------------------------------------------
Physical mail: Dr. Michael F. Crowley
Department of Molecular Biology, TPC6
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, California 92037
Electronic mail: crowley.scripps.edu
Telephone: 858/784-9290
Fax: 858/784-8688
-----------------------------------------------------------------
On Wed, 18 Feb 2004, Carsten Detering wrote:
> Hi all,
>
> I am calculating a system with ~4600 atoms (heavy atoms and hydrogens)
> on a dual Xeon in parallel mode.
> When running a molecular dynamics calculation with sander, after five
> seconds or so, the calculation always crashes, and the output is this:
>
> * NB pairs 24228 99985392 exceeds capacity ( 100000000) 0
> SIZE OF NONBOND LIST = 100000000
> EWALD BOMB in subroutine ewald_list
> Non bond list overflow!
> check MAXPR in sizes.h
>
> I have increased the value for MAXPR already, but when I make it too
> big, I get a segmentation fault by sander, or the compilation will not work.
> What is the problem here?
>
> I tried to run a long minimization, and the minimization did not crash,
> but the output looks strange, the energies do not change anymore after
> 50 steps:
>
> Here is the input file:
>
> minimization
> $cntrl
> imin = 1, maxcyc = 300 (respectively 1000),
> ntpr = 20, scee = 1.2
> nsnb = 999999, ntmin =2
> $end
>
> ....
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -8.8918E+06 4.2286E+09 6.4764E+11 O1P 4625
>
> BOND = 37586.0882 ANGLE = 1127.6320 DIHED =
> 2541.7878
> VDWAALS = 8171.2377 EEL = -122991.4496 HBOND =
> 0.0000
> 1-4 VDW = 1047.4498 1-4 EEL = -8819234.6944 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 20 -9.4025E+05 4.1863E+07 6.4114E+09 HO'2 4651
>
> BOND = 37586.0957 ANGLE = 1127.6374 DIHED =
> 2541.7879
> VDWAALS = 8171.2377 EEL = -122991.4508 HBOND =
> 0.0000
> 1-4 VDW = 1047.4498 1-4 EEL = -867736.7681 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 40 -7.7597E+06 3.2139E+09 4.9222E+11 HO'2 4651
>
> BOND = 37586.0889 ANGLE = 1127.6332 DIHED =
> 2541.7878
> VDWAALS = 8171.2378 EEL = -122991.4513 HBOND =
> 0.0000
> 1-4 VDW = 1047.4498 1-4 EEL = -7687227.4949 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 60 -4.2454E+07 9.7463E+10 1.4927E+13 O1P 4625
>
> BOND = 37586.0878 ANGLE = 1127.6326 DIHED =
> 2541.7878
> VDWAALS = 8171.2378 EEL = -122991.4514 HBOND =
> 0.0000
> 1-4 VDW = 1047.4498 1-4 EEL = ************* RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 80 -1.0829E+08 6.3526E+11 9.7292E+13 O1P 4625
>
> BOND = 37586.0879 ANGLE = 1127.6327 DIHED =
> 2541.7878
> VDWAALS = 8171.2378 EEL = -122991.4514 HBOND =
> 0.0000
> 1-4 VDW = 1047.4498 1-4 EEL = ************* RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 100 -2.1918E+07 2.5907E+10 3.9677E+12 O1P 4625
>
> BOND = 37586.0877 ANGLE = 1127.6325 DIHED =
> 2541.7878
> VDWAALS = 8171.2378 EEL = -122991.4514 HBOND =
> 0.0000
> 1-4 VDW = 1047.4498 1-4 EEL = ************* RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 120 -3.4004E+07 6.2481E+10 9.5692E+12 O1P 4625
>
> BOND = 37586.0878 ANGLE = 1127.6326 DIHED =
> 2541.7878
> VDWAALS = 8171.2378 EEL = -122991.4514 HBOND =
> 0.0000
> 1-4 VDW = 1047.4498 1-4 EEL = ************* RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 140 -1.1804E+07 7.4779E+09 1.1453E+12 HO'2 4651
>
> BOND = 37586.0886 ANGLE = 1127.6330 DIHED =
> 2541.7878
> VDWAALS = 8171.2378 EEL = -122991.4513 HBOND =
> 0.0000
> 1-4 VDW = 1047.4498 1-4 EEL = ************* RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 160 -1.6173E+07 1.4078E+10 2.1562E+12 O1P 4625
>
> BOND = 37586.0876 ANGLE = 1127.6324 DIHED =
> 2541.7878
> VDWAALS = 8171.2378 EEL = -122991.4514 HBOND =
> 0.0000
> 1-4 VDW = 1047.4498 1-4 EEL = ************* RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 180 -1.0762E+08 6.2746E+11 9.6098E+13 HO'2 4651
>
> BOND = 37586.0881 ANGLE = 1127.6327 DIHED =
> 2541.7878
> VDWAALS = 8171.2378 EEL = -122991.4513 HBOND =
> 0.0000
> 1-4 VDW = 1047.4498 1-4 EEL = ************* RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 200 -9.3365E+06 4.6654E+09 7.1451E+11 HO'2 4651
>
> BOND = 37586.0887 ANGLE = 1127.6331 DIHED =
> 2541.7878
> VDWAALS = 8171.2378 EEL = -122991.4513 HBOND =
> 0.0000
> 1-4 VDW = 1047.4498 1-4 EEL = -9264011.4914 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 220 -2.1993E+07 2.6086E+10 3.9951E+12 HO'2 4651
>
> BOND = 37586.0883 ANGLE = 1127.6329 DIHED =
> 2541.7878
> VDWAALS = 8171.2378 EEL = -122991.4513 HBOND =
> 0.0000
> 1-4 VDW = 1047.4498 1-4 EEL = ************* RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 240 -2.9524E+08 4.7255E+12 7.2373E+14 O1P 4625
>
> BOND = 37586.0880 ANGLE = 1127.6327 DIHED =
> 2541.7878
> VDWAALS = 8171.2378 EEL = -122991.4513 HBOND =
> 0.0000
> 1-4 VDW = 1047.4498 1-4 EEL = ************* RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 260 -2.4034E+07 3.1168E+10 4.7735E+12 O1P 4625
>
> BOND = 37586.0877 ANGLE = 1127.6325 DIHED =
> 2541.7878
> VDWAALS = 8171.2378 EEL = -122991.4514 HBOND =
> 0.0000
> 1-4 VDW = 1047.4498 1-4 EEL = ************* RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 280 -5.2690E+07 1.5021E+11 2.3006E+13 O1P 4625
>
> BOND = 37586.0879 ANGLE = 1127.6326 DIHED =
> 2541.7878
> VDWAALS = 8171.2378 EEL = -122991.4514 HBOND =
> 0.0000
> 1-4 VDW = 1047.4498 1-4 EEL = ************* RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 300 -1.1049E+07 6.5472E+09 1.0027E+12 HO'2 4651
>
> BOND = 37586.0886 ANGLE = 1127.6331 DIHED =
> 2541.7878
> VDWAALS = 8171.2378 EEL = -122991.4513 HBOND =
> 0.0000
> 1-4 VDW = 1047.4498 1-4 EEL = ************* RESTRAINT =
> 0.0000
> MAXIMUM NUMBER OF F EVALUATION EXCEEDED
>
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 300 -1.1049E+07 6.5472E+09 1.0027E+12 HO'2 4651
>
> BOND = 37586.0886 ANGLE = 1127.6331 DIHED =
> 2541.7878
> VDWAALS = 8171.2378 EEL = -122991.4513 HBOND =
> 0.0000
> 1-4 VDW = 1047.4498 1-4 EEL = ************* RESTRAINT =
> 0.0000
>
>
> Thanks in advance,
>
> Carsten
>
> --
>
> Carsten Detering
> University of Washington
> Seattle, WA 98195
> Fon 206.543.5081
> Fax 206.685.8665
>
>
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Received on Wed Feb 18 2004 - 21:53:00 PST
