Hello Amber Users,
I have a silica system which I solvated it in water by "psfgen" and then
converted it to amber using "chamber" in "parmed". In coordinate file I
dont have that line at the end which shows the dimension and angles of the
box, so that I added that line by myself:
50.0000000 50.0000000 50.0000000 90.000000 90.0000000 90.0000000
the "50" that I defined is the length of my system in any direction. When I
minimized that using:
Minimize
&cntrl
imin=1,
ntx=1,
irest=0,
jfastw=4,
maxcyc=200,
ncyc=100,
ntpr=1,
ntwx=1,
cut=19.0,
ntb=1,
ntp=0,
/
The bonds start to expand (even water bonds) and then the system exploded
after about 115 frames, and I got this error:
Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.
Backtrace for this error:
#0 0x7F526F55CE08
#1 0x7F526F55BF90
#2 0x7F526EC8D4AF
#3 0x54EB9B in nb_adjust_
#4 0x5509BF in ewald_force_
#5 0x722A2D in force_
#6 0x4E897A in runmin_
#7 0x4D46A3 in sander_
#8 0x4CBF39 in MAIN__ at multisander.F90:?
Segmentation fault
Do anybody have such experience? I highly appreciate if you can help me,
Best Regards,
Hadi
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Received on Thu Mar 07 2019 - 15:30:01 PST
