> The VDW
> > interactions could have a small affect at the cutoff but this is
> effectively
> > zero by the time you have reached 10 angstroms. In our experience
> using PME
> > and a cutoff of 8 you see no measurable difference moving to 10 or 12
> > angstroms other than vastly increased computation time.
>
> It is not uncommon to see reports of long-range LJ interactions having
> effects on lipid surface tensions. See, e.g., Klauda et al, JPCB,
> 114:7830, 2010, especially section 5.2 and references therein. They
> report surface tension differences at cutoffs beyond 12 Ang. (not just
> beyond 8 Ang.)
Agreed, but this is a little confusing. I was referring to running the exact
same simulation, a PME calculation and varying cut in which, for a bilayer
at least, we see very little dependence in the results on the value of cut.
Here they are comparing two different approaches. The PME approach with a
cutoff of 12 and 3D-IPS/FFT. The IPS gives long range Lennard-Jones but is
subtly different to a direct calculation of the L-J interactions is it not?
It is also changing the underlying electrostatic model at the same time and
thus lacking a control is it not?
Maybe I am misunderstanding things here but the simple comparison of
behavior as a function of cutoff for a series of identical simulations seems
to be missing and this is what I was referring to.
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 Sat Jun 16 2012 - 10:00:02 PDT
