[gmx-users] RMSD of the same protein in different solvent boxes

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Mon Feb 5 11:31:27 CET 2007


On Monday, 5. February 2007 11:13, Afonso Duarte wrote:
> Hi to All,
> I have some simulations of the same protein in different solvents, with
> different number of atoms for each (different solvent number of atoms). I
> would like to calculate a rmsd matrix to compar the backbone of the
> different sims.
> I have tried g_rms with the -f2 option to include the second trajectory,
> however it finishes with a fatal error because teh number of total atoms is
> different in both trajectories.
> Does anybody know how to solve this question? Is it possible to produce the
> rmsd matrix in a different way?

reduce both simulations to matching atomsize, e.g. for both simulations:
make_ndx (only backbone atoms) 

trjconv ..


> Thanks in advance
> Afonso
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 Florian Haberl                        
 Universitaet Erlangen/ Nuernberg
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 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de

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