[gmx-users] Coarse-graining and tabulated non-bonded potentials - will write

Steven Kirk Steven.Kirk at hv.se
Mon Dec 3 16:17:03 CET 2007

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" <gmx3 at hotmail.com>
Subject: RE: [gmx-users] Coarse-graining and tabulated non-bonded
	potentials -	will write
To: gmx-users at gromacs.org
Message-ID: <BAY110-F32D5E7B7CD6C268A5699518E750 at phx.gbl>
Content-Type: text/plain; format=flowed

>>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
>>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 
> 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 
>>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           <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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