Thank you Mark and Justin. Yes i did check the reference of your tutorial, but its just that there are so many groups using same FF but different cut-off lengths.
amit On Sun, Nov 21, 2010 at 10:22 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > Quoting Mark Abraham <mark.abra...@anu.edu.au>: > > > On 21/11/2010 8:45 PM, Amit Choubey wrote: > > > Hi all, > > > > > > I was going through the very nicely presented tutorial by Justin (on > > > KALP-15 in DPPC). I have one question regarding the non-bonded > > > cut-offs. It seems that people use many different values of non-bonded > > > cut-off (varying from 0.9 nm to 1.2 nm or probably more). How should i > > > choose the cut-off values for my simulations ? > > > > In the first instance, by reproducing the conditions under which the > > parameters were validated. Unfortunately, most of the force fields were > > not parametrized for PME, under which they are often now used. So look > > at some papers from large well-known groups that have done something > > similar to what you want to do, judge how well they have worked, and do > > something comparable. Unfortunately, there have been little or no > > systematic studies of how accurate forcefield X plus PME needs to be to > > model reality usefully. Hopefully that will change :-) > > > > And directly related to the tutorial in question, the settings used therein > were > assigned to reproduce the study that I cite in the introductory material. > > -Justin > > ======================================== > > 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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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