[gmx-users] Coarse-graining and tabulated non-bonded potentials - will write up on the wiki
Steven.Kirk at hv.se
Mon Nov 26 13:57:37 CET 2007
Firstly, many thanks to everyone who has contributed useful advice to me
over a number of years using GROMACS.
I have performed a large number of potential of mean force calculations
for the forces acting between two approximately spherical amorphous
silica particles (various sizes < 5 nm diameter) in TIP4P water with PME
electrostatics and varying concentrations of background ions.
Now I want to 'coarse-grain' the simulation, treating each silica
particle as a single point mass, and use the interaction potential
between the particles obtained from the PMF results as a tabulated
potential in mdrun, to allow longer time- and size-scales to be
investigated (I want to examine colloidal aggregation behaviour of these
I have tabulated the PMF potential and its derivatives as a function of
centre-of-mass separation of the particles as suggested in the manual
(but I can only tabulate for COM-COM distances greater than the contact
distance [ = 2r in the hard-sphere approximation] out to some cutoff).
Will I have to add a short-distance 'hard-sphere' wall to my tabulated
I have read the appropriate section of the manual on tabulated
interactions, and am working on building an appropriate topology. IU am
assuming that my coarse-grained particles consist of the silica
particles plus a number of surface counterions in such a way that the
particles will be electrically neutral, so presumably I can set all the
entries in the tabulated potential file for the Coulomb terms to zero.
If my understanding of the manual is correct, I can then introduce my
PMF potential in one or other of the g() and h() columns, along with its
The plan is to randomly place a number of the coarse-grained particles
in a simulation box and choose an appropriate time step and thermostat
to run aggregation simulations. Some of the literature I have read
suggests timesteps of around 10^-6 s and Brownian dynamics - can anyone
comment on the advisability of these choices? I anticipate significant
aggregation within ~seconds.
Another issue is whether or not to include coarse-grained water and
explicit ions in the simulation box. Recent postings on this list have
suggested that Lagrangian dynamics should not be done in a vacuum, so
presumably the same is true for Brownian dynamics? Has anyone on the
list used 'coarse-grained' water in their GROMACS simulations
If I have extracted different tabulated potentials for each background
counterion concentration, this information is presumably 'built in' to
my extracted PMF interparticle potentials, and I shouldn't need to
include explicit counterions in my coarse-grained simulation, correct?
Thank you for reading all the way through this posting. As mentioned in
the message title, I will use and write up any advice given to me as a
draft example tutorial on the wiki, then more qualified people can
correct the (probably numerous) mistakes.
Many thanks in advance,
Dr. Steven R. Kirk <Steven.Kirk at hv.se, S.R.Kirk at physics.org>
Dept. of Technology, Mathematics & Computer Science (P)+46 520 223215
University West (F)+46 520 223299
P.O. Box 957 Trollhattan 461 29 SWEDEN http://taconet.webhop.org
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