[gmx-users] vsite as interaction site for COM of benzene
schlesi at uni-mainz.de
Fri Jun 8 19:18:36 CEST 2012
i have a more conceptional question, for using vsites as
interaction-centers for coarse-grained particles:
First the simple case:
I want to simulate one benzene molecule (atomistic - aa) in
coarse-grained (cg-) benzene (each benzene molecule as a single
particle). For the cg-cg interaction of the benzene i have calculated a
But for the aa-cg interaction I'm a little bit clueless:
I want to use the COM of the aa-benzene as an interaction-site. But
there is no vsite, which i could construct from 6 atoms.
Side-note: The vsite would not interact with the with the atoms, only
So there are two ideas:
1) Using one '3out'-vsite, which is construted from 3 non-neighbour
atoms (if we had mesitylene instead of benzene, it would be the three
C-atoms to which only hydrogens are bound). The the force from the aa-cg
interaction would be distributed to these three atoms and i would hope
that the bond-constraints would do 'the rest' (i.e. they would mimick
that the whole aa-benzene molecule interacts with the cg-particles)
2) Using two '3out'-vsites. First viste the same as in (1), the second
comes from the set of the other three C-atoms. These two vsites, should
be at the same position (more or less, for a perfect energy-minimized
benzene molecule it would be so; but i would assume the error is only
minimal). Since the potential is pair-additive, i would use for this
table potential only half of the potential, so that the potential of
both particles would add up to the 'true' potential. The forces would be
calculated from the 'half-potential'.
Big questions is now:
Are (1) and (2) equivalent?
(2) Seems like the 'right way' to do.
But (1) would be easier to implement :) But the big question is, if the
bond-constraints would correct the approximation, that only 3 out of 6
atoms have a direct interaction with the cg-particles.
The real system is a little more complex. There are fracments of
molecules where i could not really construct two vsites which would have
more or less the same position. In this case, method (1) would really help.
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