[gmx-users] rc or rlist in minimum image convention?

[Justin A. Lemkul]

Juliette N. wrote:
> 
> 
> On 24 February 2012 16:52, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Juliette N. wrote:
> 
> 
> 
>         On 23 February 2012 21:18, Mark Abraham <mark.abraham at anu.edu.au
>         <mailto:mark.abraham at anu.edu.au>
>         <mailto:mark.abraham at anu.edu.__au
>         <mailto:mark.abraham at anu.edu.au>>> wrote:
> 
>            On 24/02/12, *"Juliette N." *<joojoojooon at gmail.com
>         <mailto:joojoojooon at gmail.com>
>            <mailto:joojoojooon at gmail.com
>         <mailto:joojoojooon at gmail.com>>__> wrote:
> 
> 
> 
>                On 23 February 2012 20:07, Mark Abraham
>             <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
>                <mailto:Mark.Abraham at anu.edu.__au
>             <mailto:Mark.Abraham at anu.edu.au>>> wrote:
> 
>                    On 24/02/2012 10:55 AM, Juliette N. wrote:
> 
>                        Hi all,
> 
>                        My average size is 2.9 nm obtained from NPT under
>                 large
>                        pressure and now I intend  to increase rc to 1.4
>                 and rlist to
>                        1.65 nm. I am just worried about violating
>                 minimum image
>                        convention.
> 
> 
>                    That probably violates the parametrization of your
>             force field.
> 
>                Thanks Mark. You mean rc =1.4 for OPLS-AA is not
>             appropriate? In
>                the original OPLSAA:   Optimized Intermolecular Potential
>                Functions for Liquid Hydrocarbons
>                I see rc of 15 A has been used for alkanes which requires
>             rlist of
>                around 15+2.5+17.5 A ! Please comment why I am violating
>                parametrization? Thanks.
> 
>                 It is appropriate to use a set of .mdp parameters that
>         most closely
>            reproduce the parametrization conditions, or other conditions
>         that
>            have been shown to be effective. So if you were using rc<1.4
>         and now
>            want to use rc=1.4, then it is likely that at least one of those
>            choices is inappropriate. If 1.5nm was used in parameterization,
>            then both the foregoing are probably unsuitable. The values for
>            other rxxx parameters should be addressed in that work, and will
>            depend on charge group size and electrostatics model.
> 
> 
>         Thank you Mark. I was using rc =1.1 and just wanted to how much
>         my results vary by applying rc of 1.4 nm. I dont know the exact
>         value that was used in parametrization. I have just seen some
>         previous works with cut offs around these values. Is there
>         anyway I can obtain plot of LJ potential versus distance?
> 
> 
> 
>     For any sigma and epsilon values, you can obtain such a plot with
>     g_sigeps.
> 
>     The problem with the original OPLS parameterization was that
>     different cutoffs were used for different types of molecules.
>      Shifted potentials were used instead of PME, which can change the
>     way electrostatics are handled if using the latter method.  Probably
>     someone, somewhere along the way, has published recommendations for
>     normal use in whatever type of system you're dealing with.
> 
> 
> Thank you Justin.
> 
> 1- The input values to g_sigeps has to be the geometric mean of two 
> materials then?
> 

I think g_sigeps is designed to produce simple plots for single atom types, but 
I suppose you can tweak it.  If you're looking for a simple difference in energy 
based on distance, you can do that in a few moments with a calculator and the 
Lennard-Jones equation.

> I have also another trivial question. The OPLS 1984 paper, Optimized 
> Intermolecular Potential Functions for Liquid
> Hydrocarbons states:
> 
> The cutoff distance for the intermolecular interactions was a little 
> less than half the average length of an edge of the periodic
> cube. It ranged from 9.5 A, for methane to 13 A, for benzene and 15 A, 
> for n-hexane.
> 
> My enquiry is that,
> 
> 2-is this cutoff mentioned above the parametrization cutoff or the 
> cutoff that has only been used in that paper?
> 

Hence the problem with using OPLS, in some cases.  That paper was probably for 
the old OPLS-UA parameters (which are part of Gromacs, but are outdated) and 
exemplifies how each system differed in terms of cutoffs.

> 3- If thats the cutoff that was used in parametrization, since atom 
> types of hexane, propane, heptane, ....and even saturated polymers 
> C-C-C-C........C are identical in atp file, does this mean for all 
> alkanes and such polymers  rc =15 A must be used?
>  

Again it depends on the nuts and bolts of the simulation.  The paper you cite is 
quite old and thus more modern algorithms for electrostatics, energy 
conservation, etc were not available.  I'd do some digging into more recent 
literature from people who have done similar things to see what they recommend. 
  For proteins, rc=rvdw=rlist=1.0 works well in conjunction with PME for 
electrostatics.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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