[gmx-users] Repeating the simulation

[Tsjerk Wassenaar]

Hi QIU YI HUAN,

Radius of gyration is a configuration dependent property. You need
statistics for that, so you should have more simulations. Jochens
example of the rdf is one where the statistics comes from the number
of molecules in your system (quite a number for water, versus one
self-assembled system in your case).

Cheers,

Tsjerk

On 11/6/08, Q. Y. HUAN <scottiehuan at yahoo.com> wrote:
> Dear all,
>
>  What if the analysis is radius of gyration for a self-assembled system?
>  Should I repeat it?
>
>  Sorry for the trouble.
>  Thanks
>
>
>  QIU YI HUAN
>  DEPARTMENT OF CHEMISTRY,
>  FACULTY OF SCIENCE,
>  UNIVERSITY PUTRA MALAYSIA,
>  MALAYSIA.
>
>
>
> --- On Thu, 11/6/08, Jochen Hub <jhub at gwdg.de> wrote:
>
>  > From: Jochen Hub <jhub at gwdg.de>
>  > Subject: Re: [gmx-users] Repeating the simulation
>  > To: scottiehuan at yahoo.com, "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>  > Date: Thursday, November 6, 2008, 3:38 PM
>
> > Q. Y. HUAN wrote:
>  > > Dear all gmx-users and developers,
>  > >
>  > >  I have completed a simulation, and get all the
>  > results. Just asking you guys for your opinion whether I
>  > should repeat the simulation again 1 or 2 times in order to
>  > make sure the simulation results are valid for my work even
>  > thought I have equilibrate my system before running the
>  > production simulation or I just need to do it ONCE?
>  >
>  > That depends very much on the observable that you measure
>  > and on the
>  > amount of statistics you can extract from your single
>  > simulation. E.g.,
>  > if you want to compute the RDF of water moleucles in a pure
>  > water
>  > simulation, the single simulation is certainly enough. If
>  > you observed
>  > some transition in a protein simulation only once in your
>  > simulation, it
>  > is highly advisable to repeat the simulation a couple of
>  > times to make
>  > sure that your observation is significant.
>  >
>  > Best, Jochen
>  >
>  >
>  > >
>  > > Thanks for any comments and suggestions.
>  > >
>  > > QIU YI HUAN
>  > > DEPARTMENT OF CHEMISTRY,
>  > > FACULTY OF SCIENCE,
>  > > UNIVERSITY PUTRA MALAYSIA,
>  > > MALAYSIA.
>  > >
>  > >
>  > >
>  > > _______________________________________________
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>  > > .
>  > >
>  >
>  >
>  > --
>  > ************************************************
>  > Dr. Jochen Hub
>  > Max Planck Institute for Biophysical Chemistry
>  > Computational biomolecular dynamics group
>  > Am Fassberg 11
>  > D-37077 Goettingen, Germany
>  > Email: jhub[at]gwdg.de
>  > Tel.: +49 (0)551 201-2312
>  > ************************************************
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623