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

[Juliette N.]

On 24 February 2012 16:52, Justin A. Lemkul <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 <mark.abraham at anu.edu.au>>> wrote:
>>
>>    On 24/02/12, *"Juliette N." *<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 <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 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?

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?

Appreciate your comments :)
Best
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