[gmx-users] g_clustsize problem

[David van der Spoel]

Wang Zhun wrote:
> Hi,
> 
> I'm working on peptide folding with GMX3.2.1 now. When I carried out g_clustsize, it says:
> Group     1 (     Protein) has   211 elements
> Group     2 (   Protein-H) has   167 elements
> Group     3 (     C-alpha) has    22 elements
> Group     4 (    Backbone) has    66 elements
> Group     5 (   MainChain) has    89 elements
> Group     6 (MainChain+Cb) has   108 elements
> Group     7 ( MainChain+H) has   112 elements
> Group     8 (   SideChain) has    99 elements
> Group     9 ( SideChain-H) has    78 elements
> Group    10 ( Prot-Masses) has   211 elements
> Group    11 ( Non-Protein) has 20439 elements
> Group    12 (         SOL) has 20439 elements
> Group    13 (       Other) has 20439 elements
> Select a group: 1
> Selected 1: 'Protein'
> Last frame       4000 time 20000.000
> cmid: 1, cmax: 1, max_size: 211
> Fatal error: Lo: 0.000000, Mid: 1.000000, Hi: 1.000000
> What's the meaning of the last two lines?

there is only one cluster, which is logical since you have one molecule. 
  you probably want to use g_cluster
> Thank you in advance!
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se
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