[gmx-users] rc or rlist in minimum image convention?
joojoojooon at gmail.com
Sat Feb 25 02:07:28 CET 2012
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
>>> 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
>> 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
I have also another trivial question. The OPLS 1984 paper, Optimized
Intermolecular Potential Functions for Liquid
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
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 :)
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