[gmx-users] A question on g_gyrate

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Thu Jul 7 04:03:55 CEST 2005

> When I run a job in a single node and measure radius of gyration 
> (g_gyrate), I was able to have reasonable Rg. But, when I run 
> a job in 
> multiple nodes (parallel jobs), I couldn't have reasonable Rg and it 
> was much higher.  I cannot understand why it happened.   If 
> this is the 
> case, could you tell me how to measure Rg when I run parallel 
> simulations?

Is the body that you are measuring the radii of gyration of crossing the
PBC?  If it does, then g_gyrate gives out garbage, you have to ensure
that all the molecules within the aggregate don't jump across the PBC.

Catch ya,

Dr. Dallas Warren
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 9073
When the only tool you own is a hammer, every problem begins to resemble
a nail.

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