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

[Amit Choubey]

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 <jalemkul at vt.edu> wrote:

> 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
>
> ========================================
>
> 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 at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101121/a45c25b0/attachment.html>