[gmx-users] center of mass

Qi Sun qsun at ucdavis.edu
Wed Jun 9 05:36:42 CEST 2004

At 09:09 AM 6/9/2004 +1000, you wrote:
>>consider the whole molecule as single super atom. Right now the index 
>>file can consider each atoms as separate points, I am more interested in 
>>the whole molecule together. Is there a algorithm somewhere can solve 
>>this problem?
>Is there a central atom that you can chose to be the of the entire 
>molecule and measure the RDF from that?

Thanks for your comments. Your idea is definitely right for some molecules 
like N,N-dimethyl-formamide, I will use the N atoms as the center of the 
whole molecules as you suggested. For another solvent in my system: 
Cyclohexane with a cyclic structure is impossible to find a atom at the 

>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 
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