VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Tue May 11 2004 - 10:05:08 CDT

On Tue, 11 May 2004, Dieter Blaas wrote:

> When trying to render a surface of a virus with ~
> 350.000 coordinates I get the messages shown below,
> then, after an awful lot of time an error message
> appears saying something like "the program has made
> an address exception....", the PC freezes and can only
> be re-started with RESET. Win2k, 375 MB, HD free
> space 11 GB:
> Is there an upper limit for the number of coordinates to
> be handled?
> What can I do? Thanx for help, Dieter
> .....................
> vmd > Info) Using plugin pdb for structure file F:/all_60_
> h2.pdb
> Info) Using plugin pdb for coordinates from file
> F:/Programme/F77/G77/bin/all_60
> _h2.pdb
> Info) Determining bond structure from distance search
> ...
> Info) Analyzing structure ...
> Info) Atoms: 362827
> Info) Residues: 45360
> Info) Waters: 0
> Info) Segments: 1
> Info) Fragments: 180 Protein: 182 Nucleic: 0
> Info) Finished with coordinate file
> F:/Programme/F77/G77/bin/all_60_h2.pdb.
> Reading 362827 atoms..done
> Probe radius = 3.000
> Constructing solvent-accessible surface ..

hmmm,

asking to compute the SAS for so many atoms on
such a small machine is asking for trouble.
i'd guess your machine swapped itself to death.

even if the computation of the SAS worked, it is
unlikely, that your machine will survive the
handling of the grid points. just the storage of
the atoms coordinates in single precision floating
point variables will eat over 40MB.

it would be interesting to see, where the real
internal limits of vmd in terms of grid points
and number of atoms really are. perhaps john
can comment on that.

axel kohlmeyer

> Max edge length = 1.200
> Malloc of zero or illegal length!!
> length = 0
> Malloc of zero or illegal length!!
> length = 0
> ..............................find_sol_cons() warning: sol is
> somewhat away from
> vertex (0.001048).
> .......................................find_sol_cons() warning: sol is
> somewhat
> away from vertex (0.001038).
> find_sol_cons() warning: sol is somewhat away from
> vertex (0.001904).
> ...................find_sol_cons() warning: sol is somewhat
> away from vertex (0.
> 003807).
> .................find_sol_cons() warning: sol is somewhat
> away from vertex (0.00
> 3555).
> ...............find_sol_cons() warning: sol is somewhat away
> from vertex (0.0018
> 41).
> ........................find_sol_cons() warning: sol is somewhat
> away from verte
> x (0.001221).
> ........find_sol_cons() warning: sol is somewhat away
> from vertex (0.002722).
> ...find_sol_cons() warning: sol is somewhat away from
> vertex (0.004053).
> .........find_sol_cons() warning: sol is somewhat away
> from vertex (0.003754).
> ...find_sol_cons() warning: sol is somewhat away from
> vertex (0.001486).
> ..........find_sol_cons() warning: sol is somewhat away
> from vertex (0.002303).
> ..find_sol_cons() warning: sol is somewhat away from
> vertex (0.001241).
> ..............find_sol_cons() warning: sol is somewhat away
> from vertex (0.00230
> 0).
> ..find_sol_cons() warning: sol is somewhat away from
> vertex (0.010190).
> .....find_sol_cons() warning: sol is somewhat away from
> vertex (0.001572).
> ..................find_sol_cons() warning: sol is somewhat
> away from vertex (0.0
> 02974).
> .
>
>
>
>
>
> 

-- 
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Dr. Axel Kohlmeyer                        e-mail: axel.kohlmeyer_at_rub.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
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