[gmx-users] g_gyrate

[David]

On Thu, 2003-09-25 at 08:21, Dallas Warren wrote:
> I am running g_gyrate on a number of aggregates of small molecules.  With 
> some the radius of gyration that it provides jumps around a bit, which 
> isn't unexpected as the molecules move around and rearrange.  However, at 
> some points in the the jump is quite significant, falling from 2.0 to 1.3 
> nm and staying there for several nanoseconds.  Visualizing these aggregates 
> with VMD, I can't see anything happening that is dramatic enough to justify 
> such a variation, especially down to that scale.  Measuring the inter-atom 
> distance for atoms on either side of the aggregate does not drop to such a 
> low value.
> 
> Something to do with the g_gyrate?
> 


just periodic boundary conditions.

try running 

trjconv -pbc cluster 

to cluster your aggregates together before analysis.


> This is using version 3.1.99_20021031.
> 
> Catch ya,
> 
> Dr. Dallas Warren
> Research Fellow
> Department of Pharmaceutical Biology and Pharmacology
> Victorian College of Pharmacy, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at vcp.monash.edu.au
> +61 3 9903 9083
> --------------------------------------------------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a nail.
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++