On 24 February 2012 16:52, Justin A. Lemkul <[email protected]> wrote: > > > Juliette N. wrote: > >> >> >> On 23 February 2012 21:18, Mark Abraham <[email protected] <mailto: >> [email protected].**au <[email protected]>>> wrote: >> >> On 24/02/12, *"Juliette N." *<[email protected] >> <mailto:[email protected]>**> wrote: >> >>> >>> >>> On 23 February 2012 20:07, Mark Abraham <[email protected] >>> <mailto:[email protected].**au <[email protected]>>> 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
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
