Dear all,
I would have the following question concerning the way of how to
skillfully introduce the constraints/restraints in an AMBER simulation.
We are simulating a DNA fragment attached to a surface and at the same
time sitting in kind of cup, for the surface isn't uncreased, but it
contains the cups I've just mentioned, where the cups' bottoms do
contain the linkers holding the DNA fragments attached.
We are interested in comparing the DNA's trajectory in the conventional
solution with that within such a cup, as described.
Our actual idea would be freezing-out the dynamics of the DNA linker
atom attached to the surface, to avoid constructing a fragment of
explicit inorganic surface with its explicit chemical bonding to DNA. If
dealing with such a problem, we might run into severe problems with the
force-field (re)parameterization.
For the same reason we would like to skip building-up the explicit
cups, but, instead, to constrain water molecules situated on the X- and
Y-borders of the hydrated unit cell. This way we would retain all the
features of the PBC simulation, while modelling some more or less rigid
walls in the X- and Y-directions around the DNA fragment.
Could you please assist us in correctly formulating the pertinent AMBER
input files?
Should introduce restraints/constraints BEFORE the
energy-minimization-equilibration stage or AFTER it, to produce the
restrained/constrained DNA trajectory from ONE AND THE SAME starting
point, as in the case of the conventional unconstrained solution?
Respectfully yours,
Evgeni B. Starikov
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 21 2017 - 07:00:04 PDT
