[gmx-users] Re: Simulation of 2D lattice model

James Starlight jmsstarlight at gmail.com
Thu Jan 17 10:59:09 CET 2013


thank you for so detailed explanation.  Now it's only intresting to me
if it possible to change vdw radius (assuming it as the distance from
center of atom to it outer electronic shell)? E.g I want to change
such value for each node in my lattice model (e.g for CH2 united atom
that value might be > 1.5 and I want dicrease it to the 1 A ( as for
simple carbon). Might I do it via some simplest modifications in the
nonbonded.itp or should I do that by means of changes in
sigma/epsillon terms (Which I also must express from A(c6) and B(c12)
based on gromac's combination rules) ?


2013/1/6 Bogdan Costescu <bcostescu at gmail.com>:
> On Sun, Jan 6, 2013 at 1:44 PM, James Starlight <jmsstarlight at gmail.com> wrote:
>> I mean absence of exponential factor in the C6 term :)
>> So to change the vdw radius of the specified atom I should to varry
>> both c6 and c12 shouldn't it ?
> Hmm, to me these look like very basic force field questions. Did you
> try to look the Lennard-Jones potential in a good MD book ? Or in the
> vast amount of resources available for free online ? Or, even better,
> in the GROMACS manual ? That would take surely less than an hour,
> while your questions on the subject have stretched over several days.
> The 6-12 LJ potential is composed of an attractive and repulsive term.
> The 6-12 combination is often used because of computational
> efficiency, as the 12-term can be obtained by multiplying the 6-term
> with itself. Each of these terms has a constant, typically called C6
> and C12, which tells how much each term contributes to the total
> potential. For example, to have only the 6-term, C12 can be set to
> zero - this is useful when one knows how much attractive and how much
> repulsive the potential should be. Most often though, one thinks of
> the LJ potential in terms of equilibrium distance (obtained through a
> combination rule) and potential well, expressed through the sigma and
> epsilon constants. The two pairs (C6/C12 and sigma/epsilon) are
> interrelated. The relation is given in the GROMACS manual, on the
> Wikipedia page related to the LJ potential and in many other places.
> GROMACS also comes with a tool (g_sigeps) which allows an easy
> transformation between them. As you can see from the formulas, sigma
> depends on both C6 and C12 and epsilon depends on both C6 and C12. So,
> to partly answer your question, to change the equilibrium distance
> (sigma) you need to vary both C6 and C12. It's only partly answered
> because you need to read about combination rules in the GROMACS manual
> to see how to get from the atom radius to LJ potential sigma...
> Please note that a particular force field uses only one of the pairs
> (C6/C12 or sigma/epsilon) - you can't mix and match. If you want to
> use f.e. OPLS-AA, all LJ interactions are expressed using the
> sigma/epsilon pair. If you want to introduce in this force field a new
> type of interaction based on another force field which is defined
> using the C6/C12 pair, you have to perform the conversion to
> sigma/epsilon. If, on the other hand, you design your own force field,
> you are free to use either of the two pairs but, once chosen, you have
> to be consistent and use that pair for all LJ interactions.
> Cheers,
> Bogdan
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