VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Jul 22 2012 - 23:46:35 CDT

On Mon, Jul 23, 2012 at 5:06 AM, satya kumar <mail2mvskumar_at_gmail.com> wrote:
> Hello All,
>
> I am a VMD user, experiencing an issue with reading coordinates in VMD from
> a Gromacs file. Sample coordinate from GRO file is:
>
> 1OHX OW 5231 -0.543 -2.5801000.000
> 1OHX HW1 5232 -0.510 -2.5471000.110
>
> where the "position (in nm, x y z in 3 columns, each 8 positions with 3
> decimal places)". {X,Y,Z} = {-0.543, -2.580, 1000.00} and {X,Y,Z} = {-0.510,
> -2.547, 1000.110}. When we view in VMD, these numbers are multiplied with a
> factor 10 to convert to Angstrom, then in particular Z coordinates are
> converted to 000 and 0.110 respectively. In VMD the above coordinates taken
> as:
>
> {-5.429999828338623 -25.801000595092773 0.0}
> {-5.099999904632568 -25.47100067138672 1.100000023841858}
>
> These create problems with respect to analysis, in particular the Z
> coordinate. Can someone guide me to fix this issue.

you have to fix the gromacs plugin reader to not use
a simple scanf() call to parse coordinates in .gro files,
but split the columns first and then parse the numbers.
same as the .pdb molfile plugin does.

... or you simply use a (different) file format where
these issues don't show.

axel.

>
> Thanks,
> Satya.
>
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.