Hi Peter,
The WAT label is the default in leap, but that is all. It just sets an
alias of sorts so that any references to something else (like TP3 or
something) gets recognized as WAT. I think it is safe to say that this is
standard practice as far as that means anything, but I would not be
surprised if regular users (like myself) have files that use something
different (like T4E for TIP4P-Ew).
Regards,
Brian
On Mon, Feb 13, 2012 at 6:42 PM, Peter Eastman <peastman.stanford.edu>wrote:
> Thanks David, that helps a lot. I've studied define_frames() some more,
> it appears to me the rules are as follows:
>
> 1. For four site water, the extra point always lies along the axis of the
> molecule, and the distance from the oxygen is determined by the length of
> the bond.
>
> 2. For five site water, the extra points lie above and below the central
> axis, again at a distance set by the bond length. The angle they make with
> the H-O-H plane is hardcoded as 54.735 degrees, which corresponds to TIP5P.
>
> If those are correct, I think I'm all set.
>
> One other question: is it safe to assume that water molecules will always
> be called "WAT" in prmptop files?
>
> Peter
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Brian Radak : BioMaPS
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Received on Tue Feb 14 2012 - 09:00:03 PST
