[AMBER] Problems with cutoff (?)

From: Margarita I. Bernal-Uruchurtu <mabel.uaem.mx>
Date: Fri, 11 Jan 2019 10:48:21 +0100


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

It exits with the following message:
Program received signal SIGSEGV: Segmentation fault - invalid memory

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

  imin=0, iwrap=1
  irest=0, ntx=1,
  nstlim=1000, dt=0.0005,
  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
Margarita I. Bernal-Uruchurtu
Centro de Investigaciones Química, UAEM
+52.777.329.7000 ext 6003
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Received on Fri Jan 11 2019 - 02:00:02 PST
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