[gmx-users] Re: Issue with GROMACS file format

[Justin Lemkul]

On 7/23/12 12:53 PM, SatyaK wrote:
> Thanks for the reply. In fact, I had followed the fixed format of Gromacs
> during the conversion. Below is the sample data, where I have just the
> {X,Y,Z}:
>
>   2171OHX     OW 5231  -0.543  -2.5801000.000
>   2171OHX    HW1 5232  -0.510  -2.5471000.110
>
> Z coordinate is 1000.000 and 1000.110 respectively in the above two lines.
> However, in VMD the Z coordinate is read as 000 and and 000.110 which is
> then multiplied by a factor of 10 to convert them to A. In VMD, the Z
> coordinate is read as 000*10 = 0 and 000.110*10 = 1.10. (Here the decimal
> places do not seem to be aligned, but they are aligned in the gro file that
> I created).
>

While the lines above do follow the prescribed format, perhaps VMD assumes that 
there is at least one space between all coordinate entries.  Normally one would 
not deal with such large quantities in .gro files and all columns are separated 
by at least one white space, so you may need to use a different format that can 
accommodate large values.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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