On 19/12/13 23:31, Justin Lemkul wrote:
On 12/19/13 6:14 PM, rdwducl wrote:
Thanks for the reply Justin but I'm confused. Why must the atoms be
bonded?
Ultimately I plan to model micellisation whereby surfactants, which only
interact with each other via non-bonded terms, are driven to
aggregate by
this nonpolar term...
I'm making a somewhat educated guess based on what you're observing.
A trivially simple test is to run two calculations with two particles
in a box - one in which a bond is defined between them, and one in
which there is no bond, but the atoms are at the same distance. If
the results are different, my suspicion is confirmed (that the
topology controls whether or not two atoms impact one another's
surface accessibility).
Give that a try and see what happens.
-Justin
You appear to be correct.
In the md.log file /without/ any bonds:
Computing: M-Number M-Flops % Flops
-----------------------------------------------------------------------------
NB VdW [V&F] 0.003682 0.004 49.2
NS-Pairs 0.000056 0.001 15.7
CG-CoM 0.000014 0.000 0.6
Virial 0.000104 0.002 25.0
Stop-CM 0.000014 0.000 1.9
Calc-Ekin 0.000021 0.001 7.6
-----------------------------------------------------------------------------
Total 0.007 100.0
-----------------------------------------------------------------------------
whereas when a bond is added:
Computing: M-Number M-Flops % Flops
-----------------------------------------------------------------------------
Born radii (HCT/OBC) 0.000244 0.045 96.5
Born force chain rule 0.000024 0.000 0.8
NS-Pairs 0.000001 0.000 0.0
CG-CoM 0.000002 0.000 0.0
Virial 0.000047 0.001 1.8
Stop-CM 0.000004 0.000 0.1
Calc-Ekin 0.000004 0.000 0.2
Lincs 0.000003 0.000 0.4
Constraint-V 0.000004 0.000 0.1
Constraint-Vir 0.000001 0.000 0.1
-----------------------------------------------------------------------------
Total 0.046 100.0
-----------------------------------------------------------------------------
So an atom will only 'see' another atom in computing the nonpolar term
if it is bonded to it? That doesn't make sense in my mind. What am I
missing?
Much appreciated.
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