[gmx-users] radial distribution function

[Justin A. Lemkul]

Moeed wrote:
> Thank you Justin for your reply. Simulation is 5 ns long ( before this a 
> 500 ps NVT was done as equilibration) and total energy has been 
> equilibrated after around 3 ns.
> 
>  -b is set to 4000 that is the last 1 ns has been used for rdf.
> 

For all but the simplest systems this simulation length and data analysis period 
is insufficient.  How big is your polymer?  Proper sampling may take tens to 
hundreds of ns of data collection.

-Justin

> Best,
> moeed
> 
> On Fri, Sep 9, 2011 at 3:37 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Moeed wrote:
> 
>         Dear users,
> 
>         I have created radial distribution function plot for Carbon
>         atoms in a system containing polymer chains. I see some little
>         jumps between first and second peak.
>         I need your help to comment on how this behavior can be
>         justified (or if the plot is wrong).
> 
>         g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx –b xxx
> 
> 
>     How long is the sampling?  In the absence of -e and with -b being
>     hidden from us for some unknown reason, it's hard to guess.  I'd say
>     your simulation just isn't fully converged, although for complex
>     systems that can be a challenge anyway. Nothing unusual.
> 
>     -Justin
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/__mailman/listinfo/gmx-users
>     <http://lists.gromacs.org/mailman/listinfo/gmx-users>
>     Please search the archive at
>     http://www.gromacs.org/__Support/Mailing_Lists/Search
>     <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
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
>     <http://www.gromacs.org/Support/Mailing_Lists>
> 
> 

-- 
========================================

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

========================================