[gmx-users] Coarse-graining and tabulated non-bonded potentials - will write up on the wiki

Steven Kirk Steven.Kirk at hv.se
Mon Nov 26 13:57:37 CET 2007

Hello all,

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 
appropriate derivatives.

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 
(references needed)?

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,
Steve Kirk
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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