From: Andrew Korostelev <korostel@ch...> - 2002-09-27 03:37:48
I am a recent user of APBS. The software runs perfectly alright with a
test examples (I used actin-dimer). However when I change the flag for
"calcforces" from 0 (default) to 1 or 2, the program stops after
execution of a previous command (energy calculation) with a message:
VASSERT: ASSERTION FAILURE! filename vpmg.c, line 1991
This is critical for me to be able to obtain forces for each atom, so I
need to solve the problem.
Platform in use - Linux.
Please let me know how to cure this.
From: Nathan A. Baker <baker@ch...> - 2002-09-27 13:32:42
Hi Andrew --
Thanks for your interest in APBS. First, I'd like to suggest that you
upgrade to version 0.2.2; this won't solve the particular problem that
you describe, but it does contain some other bug fixes that might be
useful. Second, this ASSERT failure is due to the fact that APBS
doesn't currently compute forces from solutions to the nonlinear PBE.
I must have written that chunk of code on a bad day as it doesn't
contain any warning messages to the user -- it simply exits with an
VASSERT failure. Sorry about that.
Nonlinear PBE forces aren't implemented because there simply isn't
much demand for them; the NPBE takes a bit longer to solve and most
force evaluation applications (minimization, molecular dynamics) are
sensitive to the speed of the algorithm. If there's a definite need
for NPBE forces, I'll go ahead an implement them. In any case, I'll
definitely add a more informative warning message to that routine --
thanks for pointing it out.
Andrew Korostelev <korostel@...> (09-26-2002 21:34:54-0400):
>I am a recent user of APBS. The software runs perfectly alright with a
>test examples (I used actin-dimer). However when I change the flag for
>"calcforces" from 0 (default) to 1 or 2, the program stops after
>execution of a previous command (energy calculation) with a message:
>VASSERT: ASSERTION FAILURE! filename vpmg.c, line 1991
>This is critical for me to be able to obtain forces for each atom, so I
>need to solve the problem.
>Platform in use - Linux.
>Please let me know how to cure this.
>apbs-users mailing list
End of message from Andrew Korostelev.
Nathan A. Baker, Assistant Professor
Washington University in St. Louis School of Medicine
Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology
700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110
Phone: (314) 362-2040, Fax: (314) 362-0234