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 - 19:53:01 PST
