[gmx-users] Repeating the simulation

[Q. Y. HUAN]

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
> ************************************************