On Thu, Oct 15, 2020, Állan Ferrari wrote:
>
>I have provided the files (prmtop, ncrst, rst7 and mdin and
>min-1.out/nvt.out outputs from my attempts to run minimization and
>equilibration) here
Thanks. Here's what I did:
1. Used sander to run a minimization; found a segfault after step 200.
(I was using the default value of ncyc.)
2. Repeated calculation 1 with macyc=200, so the code would stop before
the crash.
3. Ran cpptraj on the results of step 2, with the check option:
Warning: Atoms 66:SQL_1.H41 and 82258:WAT_27549.H2 are close (0.00)
Looking at the prmtop file (using parmed) I see that H41 has a charge of
-1.2 (!) which seems way wrong. In fact, all the charges seem way too
large -- you have aliphatic carbons with a charge of +2 and hydrogens
with charges of -1 (about). All charges for a saturated hydrocarbon
should be near zero -- say with hydrogens about +0.1.
This probably leads to an unstable potential energy surface, and that will
need to be fixed.
...I hope this helps in your debugging process.....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Oct 18 2020 - 06:00:04 PDT
