On 23 February 2012 21:18, Mark Abraham <[email protected]> wrote:
> On 24/02/12, *"Juliette N." *<[email protected]> wrote: > > > > On 23 February 2012 20:07, Mark Abraham <[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? > > Mark > > > > > >> >> >> 1- My question is which of rc or rlist is important for minimum image >> convention? >> >> >> The larger one. See manual 3.2.2. >> >> >> If its rlist then I think I have to make a bigger system. >> >> 2- Will the simulation raise warning once half of the box size < rc or >> (rlist) ? I mean I want to make sure than over the course of simulation I >> am not breaching this rule. >> >> >> Under at least some circumstances such volume changes cause fatal errors. >> You can check for such after the fact with g_mindist -pi >> > > >
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