[gmx-users] Coarse-graining and tabulated non-bonded potentials - will write
gmx3 at hotmail.com
Mon Nov 26 14:18:36 CET 2007
>From: Steven Kirk <Steven.Kirk at hv.se>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at 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
>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
I don't really understand the issue here.
You (would) also directly get the repulsive part of the PMF from a
simulation. I assume that you mean that you have not done simulations
to obtain the PMF at shorter distances?
If not, just do so.
>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
>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
>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.
>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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