Dear Amber users and developers,
this error -
Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.
Backtrace for this error:
#0 0x2AF93041FE08
#1 0x2AF93041EF90
#2 0x2AF930C834AF
#3 0x492AFB in __nb_exclusions_mod_MOD_nb_adjust
#4 0x489A80 in __pme_force_mod_MOD_pme_force
#5 0x4B4A6C in __runmin_mod_MOD_runmin_master
#6 0x4E6197 in MAIN__ at pmemd.F90:?
ocurred on the stage of restrained minimization with SPC/E water model in
serial pmemd.
With the same system employing OPC model no errors happened.
The solute is the DNA helices.
I ran the minimization again with ntpr=1.
Here are the last 5 steps:
NSTEP ENERGY RMS GMAX NAME NUMBER
322 -3.0182E+05 3.4706E+00 6.6853E+02 HOP3 1021
BOND = 20364.6946 ANGLE = 845.6832 DIHED =
2833.2589
VDWAALS = 52481.4441 EEL = -363000.9613 HBOND =
0.0000
1-4 VDW = 1022.9308 1-4 EEL = -16400.8213 RESTRAINT =
36.9129
EAMBER = -301853.7711
NSTEP ENERGY RMS GMAX NAME NUMBER
323 -3.0335E+05 1.5408E+02 2.8214E+04 HOP3 1021
BOND = 20338.5653 ANGLE = 845.7878 DIHED =
2833.2695
VDWAALS = 52481.4633 EEL = -362999.8519 HBOND =
0.0000
1-4 VDW = 1022.9031 1-4 EEL = -17913.5356 RESTRAINT =
36.9124
EAMBER = -303391.3985
NSTEP ENERGY RMS GMAX NAME NUMBER
324 -3.1079E+05 4.2653E+03 8.4957E+05 HOP3 1021
BOND = 20337.0066 ANGLE = 845.9324 DIHED =
2833.2704
VDWAALS = 52481.4638 EEL = -362999.7104 HBOND =
0.0000
1-4 VDW = 1022.8998 1-4 EEL = -25347.4662 RESTRAINT =
36.9124
EAMBER = -310826.6036
NSTEP ENERGY RMS GMAX NAME NUMBER
325 -3.0409E+05 3.0997E+02 5.8741E+04 OP2 1025
BOND = 20335.7355 ANGLE = 846.1241 DIHED =
2833.2714
VDWAALS = 52481.4654 EEL = -362999.5573 HBOND =
0.0000
1-4 VDW = 1022.8963 1-4 EEL = -18645.1354 RESTRAINT =
36.9123
EAMBER = -304125.2000
NSTEP ENERGY RMS GMAX NAME NUMBER
326 -3.0409E+05 3.1039E+02 5.8822E+04 OP2 1025
BOND = 20335.7360 ANGLE = 846.1239 DIHED =
2833.2714
VDWAALS = 52481.4654 EEL = -362999.5574 HBOND =
0.0000
1-4 VDW = 1022.8963 1-4 EEL = -18646.8302 RESTRAINT =
36.9123
EAMBER = -304126.8946
NSTEP ENERGY RMS GMAX NAME NUMBER
327 -3.0409E+05 3.1090E+02 5.8919E+04 OP2 1025
I would like to ask you what can be source of the problem
and how is it possible to overcome it?
Kind regards,
Nick
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Received on Fri Apr 27 2018 - 08:30:01 PDT
