Hello,
I'm having a very strange problem with the cutoff option.
The system is a box with a water/air interface and a couple of organic
molecules. The starting geometry was previously equilibrated with TIP3P and
GAFF and I'll use SEBOMD and equilibrate with the lambda option.
With amber18 in a MacBookPro /Mojave it finds no problem. As soon as I
switch to the cluster I have an error that appears using both, the amber18
or amber16 versions.
Running with these options:
sander -O -i din.in -o tmp.out -c mini.start.rst7 -p mini.prmtop -ref
mini.start.rst7
It exits with the following message:
Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.
Backtrace for this error:
#0 0x7f64e7611f2f in ???
#1 0x56e1bc in ???
#2 0x56ead1 in ???
#3 0x70ef85 in ???
#4 0x52389a in ???
#5 0x4d2aa5 in ???
#6 0x4ca48b in ???
#7 0x4ca4ef in ???
#8 0x7f64e75fe11a in ???
#9 0x45ab69 in ???
#10 0xffffffffffffffff in ???
Segmentation fault (core dumped)
Looking for the possible origin of the problem I switched to an input like
this:
equilibration
&cntrl
imin=0, iwrap=1
irest=0, ntx=1,
nstlim=1000, dt=0.0005,
tempi=298.0,
temp0=298.0,
ntpr=2, vrand=10,
ntb=1, cut=8.0,
and then I changed the size of the cutoff from 8.0 to 7.0 With the smaller
cutoff it doesn't exit with an error but if I increase the size of the
cutoff from 7.4 to 7.5 then I'll get again the same error than with a
cutoff of 8.0
I'd very much appreciate your insight in this.
M. Bernal-U.
Science is built with facts as a house is with stones, but a collection of
facts is no more a science than a heap of stones is a house. - Henri
Poincaré
°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°
Margarita I. Bernal-Uruchurtu
Centro de Investigaciones Química, UAEM
+52.777.329.7000 ext 6003
mabel.uaem.mx
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Received on Fri Jan 11 2019 - 02:00:02 PST
