From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Nov 13 2012 - 10:40:42 CST
This is not a NAMD question but a charmm/amber question. The breaking of
bonds is not possible in both of them, and usually not in general for
classical forcefields, but I heard of one that is supposed to be able to.
What you are maybe interested in is QM and QM/MM hybrid solutions.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Stefanos Anogiannakis
Gesendet: Dienstag, 13. November 2012 11:15
Betreff: namd-l: Bond Breaking in Polymer Networks - United Atom Forcefield
I'm interested in performing MD simulation of polymer networks under
where some chains could break as elongation proceeds.
I use a United Atom (UA) forcefield.
The bonded interactions of my model include:
(i) a bond stretching potential
(ii) an angle potential (bond bending)
(iii) a dihedral (torsional) potential.
The nonbonded, pairwise interactions are based on a 6-12 Lennard-Jones (LJ)
which acts between all possible pairs (inter- and intra-chain),
except from intra-chain pairs that are separated by 1, 2, or 3 sequential
(the so called (1-5) intra-chain LJ potential).
I would like to ask you if NAMD is able to break bonds 'on the fly', as
according to a distance criterion for the bond length.
In terms of potentials, a bond scission event means that
(a) For the UAs making this bond, the bond potential will not be evaluated
(or will be turned off) after breakage
(b) The angle and dihedral potentials related with this bond will cease to
exist (or be evaluated)
(c) A LJ pairwise interaction between the UAs of the broken bond will start
Thank you very much for your help,
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