Quoting Mark Abraham <[email protected]>: > 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 [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
