[gmx-users] g_gyrate

Dallas Warren dallas.warren at vcp.monash.edu.au
Thu Sep 25 08:36:01 CEST 2003

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?

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.

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