[gmx-users] RMSD

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Wed Apr 25 09:28:24 CEST 2007

On Tuesday, 24. April 2007 20:23, Dhananjay wrote:
> Hello all,
> I have 10 pdb files. I want to do simulation on each of them. But before
> that I want to check RMSD of each of them with others and want to know  an
> average RMSD over all 10 srtuctures. The  pdb files are o/p of
> protein-protein docking.
> In this case, can I make use of programme g_rms for the RMSD calculations ?
> Or any other suggestion/programme please

you can also cat each file together, and than you can calculate also with 
gromacs tools (g_rms) differnet rmsd also with -m option (matrix) so you 
should have than an 10x10 matrix so also RMSD of 1 to 2, 1 to 3 ...



 Florian Haberl                        
 Universitaet Erlangen/ Nuernberg
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 Telephone:  	+49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de

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