Hi Ignacio,
> I followed your suggestion and used tleap to generate the prmtop file
> for
> Ewald. But nothing changed. So my question is, assuming I don't have
> errors
> in the preparation of the systems, does it sound reasonable to anybody
> that
> using two sets of coordinate+parameter files, with the difference that
> one
> defines a ligand alone, the other a ligand in a periodic system, but
> both
> without water, the result of the thermodynamic integration is ~2
> kcal/mol vs
> 40 kcal/mol? I guess that difference could be just the influence of the
> periodic copies on the central copy of the ligand, but doesn't it sound
> too
> much for an uncharged ligand?
I am not sure if this is reasonable or not. It is certainly possible that
normally there would be a large cancellation of errors. You can turn on
verbose in the &ewald namelist and this will give you the contributions to
the energy from the direct and reciprocal parts of the sum and this may help
give you an idea. I would also suggest looking at how things vary as a
function of the box size. If your cutoff is larger than your solute then
this should be fairly simple. As you increase the box size so the result
should converge to the pure vacuum case since with an infinite box you end
up with the vacuum calculation.
Now, if you are using something like an 8 A cut off then things are a lot
more complicated. The same holds above with box size but you only get rid of
the contribution from the images. You still have the contribution from those
atom pairs in the central box that are more than the cutoff distance apart.
You would then need to look at how the energy differs as a function of the
cutoff value.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Tue May 24 2011 - 10:00:03 PDT
