Berk Hess kindly answered my original query below. I have some more
questions that might be of general interest to the list, so I'm
conducting another step of the conversation in the list.
-----
Date: Mon, 26 Nov 2007 14:18:36 +0100
From: "Berk Hess" <[EMAIL PROTECTED]>
Subject: RE: [gmx-users] Coarse-graining and tabulated non-bonded
potentials - will write
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; format=flowed
From: Steven Kirk <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: gmx-users@gromacs.org
Subject: [gmx-users] Coarse-graining and tabulated non-bonded potentials -
will write up on the wiki
Date: Mon, 26 Nov 2007 13:57:37 +0100
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 particles).
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
potentials?
I don't really understand the issue here.
You (would) also directly get the repulsive part of the PMF from a
constraint
simulation. I assume that you mean that you have not done simulations
to obtain the PMF at shorter distances?
If not, just do so.
Yes, I have calculated the PMF at shorter distances, and it becomes
repulsive at shorter distances.
My confusion was caused by my uncertainty as to what should be in the
tabulated potential file for very short distances (tabulated potentials
must be tabulated for distances r >= 0, even if I only have real
tabulated potential data from some r_min (>0) upward). A quick check of
the example 'table6-9.xvg' file for the directory referenced in the
standard GROMACS distribution using the environment variable GMXLIB has
shown me that I can safely 'pad out' all the columns for distances 0 <=
r < r_min with zeroes.
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?
Because of the way you did things, everything is included in the PMF,
both water and counterions.
If this is an accurate approach is a completely different matter.
Now you have the 2-body coarse-grained term correct, but there
could of course be multi-body non-additive effects.
For such effects you might need coarse-grained water or counterions,
but then things get much more complicated.
I'm uncertain that if my particles have a persistent (though
fluctuating) electric dipole moment throughout the PMF runs, this will
also be fully accounted for by the PME electrostatics used during my PMF
runs. I have read a paper
1. R. Blaak, M. A. Miller, and J.-P. Hansen, “Reversible gelation and
dynamical arrest of dipolar colloids,” Europhysics Letters (EPL) 78, no.
2 (2007). doi: 10.1209/0295-5075/78/26002
where the authors have used GROMACS and added an *explicit* dipole to
colloidal particles.
Can I use such an approach in further work based on my PMF potentials,
or by doing so would I be counting the electric dipole effects twice?
You mention that things get complicated in this situation. Do you (or
anyone reading this on the list) know how to implement such 3-body terms
in GROMACS (presumably using *assumed* and unchanging bonded angular
terms where each particle becomes an 'atom' in a bigger 'molecule'), or
alternatively another free MD code that can handle both dynamic bonding
*and* multibody potentials ?
Again, many thanks in advance for all responses.
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 <[EMAIL PROTECTED], [EMAIL PROTECTED]>
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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