From: David Zhang <dzhang@mc...> - 2004-02-09 20:14:48
I am trying to use mg-dummy to calculate the solvent-accessibility of a
large molecule. It seems that APBS checks memory usage just like
solving PBE for real. So when I use a large grid (greater than
257x257x257), APBS will complain it can't allocate memory and then quit.
Is there any way to skip the memory check?
Hi David --
You're right, the current version tries to initialize all 20 N-length arrays
for a dummy calculation. This is for several reasons, including debugging.
However, I realize it's also rather annoying and will add it to my TO-DO
list for future releases. In the meantime, you might consider using the
Python-wrapped version of APBS to intialize and write out arrays; that might
Nathan A. Baker, Assistant Professor
Washington University in St. Louis
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
> -----Original Message-----
> From: apbs-users-admin@...
> [mailto:apbs-users-admin@...] On Behalf Of David Zhang
> Sent: Monday, February 09, 2004 12:15 PM
> To: apbs-users@...
> Subject: [Apbs-users] Use mg-dummy
> Hi Nathan,
> I am trying to use mg-dummy to calculate the
> solvent-accessibility of a
> large molecule. It seems that APBS checks memory usage just like
> solving PBE for real. So when I use a large grid (greater than
> 257x257x257), APBS will complain it can't allocate memory and
> then quit.
> Is there any way to skip the memory check?
> apbs-users mailing list