VMD-L Mailing List

From: fariba taghavi (faribataghavifariba_at_gmail.com)
Date: Tue May 08 2012 - 09:14:54 CDT

Hi,
  I look at those books again.
There nothing there about the "lag time" in this "diffusion coefficient
  tool" from Dr. toni giorgino.
 Any help would be helpful.
  Thanks,
  Fariba

On Tue, May 8, 2012 at 10:10 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> please always reply to the mailing list. thanks.
>
> On Tue, May 8, 2012 at 10:05 AM, fariba taghavi
> <faribataghavifariba_at_gmail.com> wrote:
> > Hi,
> > I look at those books again.
> > There nothing there about the "lag time" in this "diffusion coefficient
> > tool".
> > Any help would be helpful.
> > Thanks,
> > Fariba
> >
> >
> > On Tue, May 8, 2012 at 9:17 AM, fariba taghavi
> > <faribataghavifariba_at_gmail.com> wrote:
> >>
> >> Hi,
> >> I mean "diffusion coefficient tool" from Dr. toni giorgino.
> >> Thanks for your suggestions.
> >>
> >> Best
> >> Fariba
> >>
> >>
> >>
> >> On Tue, May 8, 2012 at 9:12 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> >>>
> >>> On Tue, May 8, 2012 at 8:06 AM, fariba taghavi
> >>> <faribataghavifariba_at_gmail.com> wrote:
> >>> > Dear vmd users,
> >>> >
> >>> > I have some questions about the diffusion coefficient plug-in in VMD.
> >>>
> >>> which plugin exactly are you referring to?
> >>> there is no such plugin bundled with VMD.
> >>> have you checked who is the author of the
> >>> plugin and contacted this person?
> >>>
> >>> > I do not know exactly the meaning of "lag times" and "analysis
> >>> > interval" and
> >>> > their differences in this plug-in.
> >>> > Why analysis interval should be bigger than time lag?
> >>> > What is the "premature conclusions"?
> >>> > What does a "subsection of the trajectory" mean in "Analysis interval
> >>> > boxes"?
> >>> > Would you please explain me or introduce me a book or paper about
> these
> >>> > concepts?
> >>>
> >>> this sounds like you need to learn some rather
> >>> fundamental concepts of analysis of MD data.
> >>> this is handled by any good text book on MD.
> >>> try "understanding molecular simulations" by
> >>> daan frenkel and berend smit, or if you like it
> >>> more technical and "old fashioned" check out
> >>> "computer simulations of liquids" by allen and
> >>> tildesley.
> >>>
> >>> axel.
> >>>
> >>> > Any help would be helpful,
> >>> > Fariba
> >>> >
> >>> >
> >>>
> >>>
> >>>
> >>> --
> >>> Dr. Axel Kohlmeyer
> >>> akohlmey_at_gmail.com http://goo.gl/1wk0
> >>>
> >>> College of Science and Technology
> >>> Temple University, Philadelphia PA, USA.
> >>
> >>
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>