On Tue, Feb 19, 2013 at 6:22 PM, Robin Betz <rbetz.ucsd.edu> wrote:
> Hi, I found the problem :)
>
> addIonsRand replaces random solvent molecules with ions, and to grab a
> solvent molecule's position uses its imaging atom. The problem is that for
> some reason TIP4P water doesn't have an imaging atom. In solvent.lib the
> entries for TIP4PEWBOX and TIP4PBOX have an imaging atom index of 0:
>
> !entry.TIP4PEWBOX.unit.residues table str name int seq int childseq int
> startatomx str restype int imagingx
> "WAT" 1 5 1 "w" 0
> "WAT" 10002 5 5 "w" 0
> "WAT" 20003 5 9 "w" 0
> ... etc
>
> Is this the expected behavior for TIP4 water? I am not sure what the
> imaging atom is actually used for as I was just using it to grab the
> position of a solvent molecule. From looking at the code I was under the
> impression that all water molecules should have an imaging atom.
>
> The TIP3PBOX gives an imaging atom for each water molecule:
>
> !entry.TIP3PBOX.unit.residues table str name int seq int childseq int
> startatomx str restype int imagingx
> "WAT" 1 4 1 "w" 1
> "WAT" 2 4 4 "w" 4
>
> ... etc
>
> I can make addIonsRand get the solvent molecules another way if this is the
> expected behavior for TIP4P boxes.
>
Indeed, the imaging atom for the water molecules in TIP4Pew Box is not
defined. Can you use the first atom of the unit instead of the imaging
atom?
Is the imaging atom actually used for anything in tleap?
Thanks!
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Feb 19 2013 - 17:00:03 PST
