On Tue, 2014-02-04 at 13:18 +0800, Nitin Sharma wrote:
> Dear amber users,
>
>
> I got error in extending simulation from a 50ns MD run restart file .
>
> ERROR: I could not understand line 11876
>
> -0.0694812 -0.0371947 -0.0775758 0.2710202 -0.5647205 -0.7658839
>
>
>
> Lines 11875, 11876 and 11877 are as follows:
>
> -309.6311297-120.7228754 -89.3867069-308.6193503-121.6398973 -88.7337458
>
> -0.0694812 -0.0371947 -0.0775758 0.2710202 -0.5647205 -0.7658839
>
> 0.3368825 0.5317549 -0.2689358 0.3489688 -0.2916539 0.1023535
>
>
>
> However, on examination I found issues on following lines 11745 and 11746
>
> 298.5346412-355.8839842 34.9198195************ 54.5942591-259.6477784
>
> ************ 55.0123119-258.9368236************ 53.6829762-259.3702980
>
>
>
> So why is the error on line 11876 instead of lines 11745 and 11746?
I'm not sure why the error was reported for line 11876. I will look
into this, but the real problem is on line 11745.
> 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
Restart files have the same format regardless of what type of simulation
you are running. If a row has only 3 numbers, that means it is the
coordinates or velocities of the last particle, and that your particle
has an odd number of atoms.
The restart file format is fully described here:
http://ambermd.org/formats.html#restart
Basically, each number is a coordinate and the coordinates are arranged
as:
X1 Y1 Z1 X2 Y2 Z2
X3 Y3 Z3 X4 Y4 Z4
...
XN YN ZN
The last 6 numbers in the file are the box lengths and angles,
respectively (if a periodic box exists).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Feb 04 2014 - 05:30:03 PST
