VMD-L Mailing List

From: Yinglong Miao (yimiao_at_indiana.edu)
Date: Mon Feb 16 2009 - 12:44:16 CST

Dear Axel,

I called VMD in NAMD simulations. But as I tested separately, it's a script
all for VMD that includes calling a package modified from and similar to
"solvate" in the tcl plugins.

Thanks,
Yinglong

On Mon, Feb 16, 2009 at 1:26 PM, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu
> wrote:

> On Mon, 16 Feb 2009, Yinglong Miao wrote:
>
> YM> Dear VMD developers/users,
> YM>
> YM> I have been running a VMD script that involves loading PSF/PDB files
> and
> YM> writing DCD files for a pretty large system (~3M atoms). The program
> seems
> YM> to run fine with files processed properly, but error messages like "***
> YM> glibc detected *** free(): invalid pointer: 0x00000000102a8f28 ***"
> keep
> YM> coming up during the program running. I am not sure whether it comes
> from
> YM> large system processing or something regarding memory. I looked it up
> in the
>
> this most certainly points to internal memory corruption.
> do you run external binaries while processing your files,
> or is this all VMD?
>
> there are a bunch of possible causes and it is generally
> hard to tell where exactly the origin is without experience
> and the proper tools.
>
> before entering a wild goose chase, can you please try running
> the same script with the latest alpha/beta binaries that john
> has posted. if the problem persists, it needs to be tracked down,
> but the details of that process are better discussed off-list.
>
> cheers,
> axel.
>
> YM> list archives but found no clue. Has anyone come into such cases? Your
> help
> YM> will be appreciated!
> YM>
> YM> Thanks!
> YM>
> YM>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
> 

-- 
Yinglong Miao
Ph.D. Candidate
Center for Cell and Virus Theory
Chemistry Department, Indiana University
800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
Tel: 1-812-856-0981