On Tue, Feb 04, 2014, Nitin Sharma wrote:
>
> As I am doing NPT simulation can someone tell me what each column of
> .rst file signifies as in another restart file I found last three
> columns missing from a partucluar line though no error was shown in
> exnteding simulation using that particular restart file
>
> -164.4358509 -80.1554899 -82.6626818-165.1554065 -79.5261355 -82.7115146
> -164.3321645 -80.3286204 -81.7269966
> 0.1816440 -0.2486005 0.1115355 0.7880025 0.3099874 -0.7650294
Your system has an odd number of atoms; since the x,y,z coordinates are
printed 6 pe line (2 atoms per line), the final line has only three entries.
> The .rst file of the one giving error had 2nd line as follows: 23746
> 0.5102000E+05 meaning 23746 number of atoms. Hence, I assume the .rst
> file should have 23748 lines but 23749 lines. When I checked same in
> case of the file .rst file with no error I got 24239 lines while number
> of atoms are 24235.
The relation between the number of atoms and the actual number of lines in
a restart file depends on whether the number of atoms is even or odd, and
whether the system is periodic or not.
This and other amber file formats are discussed here:
http://ambermd.org/formats.html
...dac
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Received on Tue Feb 04 2014 - 05:30:02 PST
