On Sun, Nov 20, 2022, Matthew Guberman-Pfeffer via AMBER wrote:
>
>I’m really puzzled by a segmentation fault error I’m getting for
>simply trying to do a vacuum minimization. Below is my input file and
>command. Note that it works fine with SANDER, but crashes with PMEMD. No
>error message is printed by PMEMD to the end of the out file (see below for
>output).
>What is going wrong? What should I check?
What happens in the sander run? Do you see bad energies at the first step?
If you want to debug pmemd with a segfault, your first step would be to
build with debugging symbols on. Add -DCMAKE_BUILD_TYPE=DEBUG to your
run_cmake file, and re-build. That will only tell you the location where
the segfault is occurring, but that might be enough.
You should note that setting ntb=0 and igb=0 enters code that is *very* rarely
used. If you want a vacuum simulation, try setting igb=6 instead.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 21 2022 - 07:00:02 PST
