[gmx-users] question on KALP-15 in DPPC tutorial

Justin A. Lemkul jalemkul at vt.edu
Sun Nov 21 19:22:04 CET 2010

Quoting Mark Abraham <Mark.Abraham at 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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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