Dear all,
(Sorry for the long email. but my problem is complicated and i cannot
shorten this.)
I am a new user of Amber, and I bumped into a very frustrating problem
in my first try of running Amber 9: SANDER keeps crashing after an
uncertain number of steps with the error message as follows:
----------error message with output context---------------
NSTEP = 17800 TIME(PS) = 37.800 TEMP(K) = 285.13 PRESS =
-656.4
Etot = -2390.0295 EKtot = 1023.2938 EPtot =
-3413.3233
BOND = 1.2793 ANGLE = 0.4961 DIHED =
0.0002
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
209.2466
EELEC = -3624.3456 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 506.8383 VIRIAL = 996.4304 VOLUME =
34547.6103
Density =
0.5226
Ewald error estimate: 0.3956E-03
------------------------------------------------------------------------------
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line
Source
sander 0000000000548A0C Unknown Unknown Unknown
sander 00000000004FAB86 Unknown Unknown Unknown
sander 00000000006BE194 Unknown Unknown Unknown
sander 00000000004DBE6B Unknown Unknown Unknown
sander 00000000004ADF9E Unknown Unknown Unknown
sander 00000000004AA218 Unknown Unknown Unknown
sander 0000000000404062 Unknown Unknown Unknown
libc.so.6 0000003BA081D8A4 Unknown Unknown Unknown
sander 0000000000403FA9 Unknown Unknown Unknown
NSTEP = 17900 TIME(PS) = 37.900 TEMP(K) = NaN PRESS
= NaN
Etot = NaN EKtot = NaN EPtot
= NaN
BOND = 1.5918 ANGLE = 0.6282 DIHED =
0.2988
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS
= NaN
EELEC = NaN EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 532.8891 VIRIAL = NaN VOLUME =
34531.6889
Density =
0.5228
Ewald error estimate: NaN
------------------------------------------------------------------------------
The whole situation is as follows:
I want to run a NVT MD at 300 K on a nitrate ion in a 600 POL3 water
cubic box with periodic boundary conditions. I first generated the
prmtop and inpcrd files using Leap. I minimized the system first, and
then heated it up from 0K to 300K using NVT MD. In the third step, I did
a NPT MD at 300 K to get the correct density (~1g/cc). It was at this
step when I found the problem. The input file is attached below together
with the command to start the simulation:
---------------input-----------------
NO3-.(H2O)600: 100ps MD NPT
&cntrl
imin = 0,
irest = 1, ntx = 7,
ntb = 2, pres0 = 0.7, ntp = 1, taup = 5.0,
ipol = 0,
cut = 12.0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 100000, dt = 0.001
ntpr = 100, ntwx = 100, ntwr = 1000
/
---------bash script to run sander--------------
sander -O -i nit_600pol3_cube_md2.in -o nit_600pol3_cube_md2.out -p
nit_600pol3_
cube.prmtop -c nit_600pol3_cube_md1.rst -r nit_600pol3_cube_md2.rst -x
nit_600po
l3_cube_md2.mdcrd
I searched the mail archive and only found a similar problem about
DIVCON, which has already been corrected by a bugfix of amber 9. this
amber 9 was compiled using intel fortran compiler 10.0.023. all bug
fixes for amber 9 had been applied before compilation.
i tried the following things:
1) changing the parameters, which didn't help at all. amber still
crashed, although not exactly after the same number steps.
2) doing the same simulation on H2O in 600 POL water box (i.e. a 601
POL3 water box), in which the same problem occurred.
3) using amber 8 (compiled with intel fortran compiler v9) and amber 7
(compiled with some other fortran compiler, but i don't know which one),
and amber 7 worked and finished the simulation, but it was slower than
amber 9, cannot do NTT=3 temperature scaling, and there was no parallel
sander i can use. amber 8 displayed the same problem as amber 9.
i wonder if anyone can kindly help me out of this frustrating situation.
thanks,
Shuzhi "James" Wang
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Received on Wed Dec 12 2007 - 06:07:33 PST
