On Monday 29 December 2003 06:14 pm, Bill Ross wrote:
> > "The format of a restart file for roar-cp MD is:
> > natoms time nlink
> > 3 times natoms position coords + 3 times nlink link atoms coords
> >
> > See file nhc_lib.F (restart file is unit 16). Search for
> > WRITE(16 this will give format."
> >
> > So it should suffice to just add the number of link atoms as a third
> > field. I'm guessing the format should be I5 in analogy with the format of
> > natoms, but you should check it yourself.
>
> If there are link atoms, it appears that you would need to
> generate coordinates for them as well as adding a 3rd field
> in the header to give the number of atoms.
>
> Bill Ross
>
You are right, in the general case. My notebook was not really clear on this
so I didn't include all of the notes, but it seems to imply that I just added
a 0 for the third field, and that satisfied roar-cp. Roar-cp reads the
number of link atoms and their atom numbers from its control file, I do
remember that much. I think it generates the link atom coordinates at
startup from the input coordinates and the information in the control file.
Looks like this whole situation is ripe for a complete review and a bit of
documentation. I'll see if I can get around to that sometime soon. Its
pretty clear roar-cp is not a widely used AMBER component. It wouldn't even
compile with the amber 7 distribution source (buggy makefile).
Bud Dodson
--
M. L. Dodson bdodson.scms.utmb.edu
409-772-2178 FAX: 409-772-1790
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Received on Wed Jan 14 2004 - 15:53:13 PST
