VMD-L Mailing List

From: Nicolas Bigaouette (nbigaouette_at_gmail.com)
Date: Thu Jul 31 2008 - 19:21:12 CDT

Haaaa.. I see ;)

I chose .gro as the file format since I wanted a simple format. I do not
know the types of atoms before iterating on them, so I need a file format
where I can specify the atom/ion/electron.

I only need positions as a function of time, with a non fixed number of
atoms. And ideally with units of Angstrom ;)
Do you have a suggestion?

Thank you

Nicolas

2008/7/31 Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>

> On Thu, 31 Jul 2008, Nicolas Bigaouette wrote:
>
> NB> [...]
> NB> But when I import them in VMD, the position are multiplied by 10, so it
> is
> NB> (0,2,2) instead of (0,0.2,0.2)
>
> NB> It did not happen with other file format (VTF). I checked the source,
> and to
> NB> my surprise there is a comment at the begining of Gromacs.h:
> NB> * o gro_rec() assumes positions in .gro files are nanometers and
> NB> * converts to angstroms, whereas they really could be any unit
> NB> and a couple of lines later, there is a degine:
> NB> #define ANGS_PER_NM 10
>
> NB> Why is it converting the file's value?? If the data file is wrong, then
> I
> NB> prefer changing it myself then having to hack VMD's code to remove the
> NB> scaling factor. The file says 0.2, I want to see 0.2 in VMD.
>
> no!!!
>
> VMD's internal units are angstrom and Gromacs uses nanometers.
> this is not wrong, but required for consistency. if you change
> this scaling factor, all hell will break loose since nothing will
> work anymore that handles molecular systems, _particularly_ real
> gromacs output. if you want the same numbers in VMD than you write
> to your files, use a file format that uses angstrom as internal units.
>
> cheers,
> axel.
>
> NB> I did a patch to change that:
> NB>
> NB> --- plugins/molfile_plugin/src/Gromacs.h.orig 2008-07-31
> NB> 19:26:41.000000000 -0400
> NB> +++ plugins/molfile_plugin/src/Gromacs.h 2008-07-31
> 19:27:11.000000000
> NB> -0400
> NB> @@ -96,8 +96,10 @@
> NB> #define MAX_G96_LINE 500 // Maximum line length of .g96 files
> NB> #define MAX_TRX_TITLE 80 // Maximum length of a title in .trX
> NB> #define MAX_MDIO_TITLE 80 // Maximum supported title length
> NB> -#define ANGS_PER_NM 10 // Unit conversion factor
> NB> -#define ANGS2_PER_NM2 100 // Unit conversion factor
> NB> +//#define ANGS_PER_NM 10 // Unit conversion factor
> NB> +//#define ANGS2_PER_NM2 100 // Unit conversion factor
> NB> +#define ANGS_PER_NM 1 // Unit conversion factor
> NB> +#define ANGS2_PER_NM2 1 // Unit conversion factor
> NB>
> NB>
> NB> // All the supported file types and their respective extensions
> NB>
>
> --
> =======================================================================
> 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.
>