[gmx-users] two questions on essential dynamics

paloureiro at biof.ufrj.br paloureiro at biof.ufrj.br
Mon Nov 21 16:48:38 CET 2005


I have a system of "n" molecules in the liquid state. I picked one type of atom 
and used it as an input group (with "n" atoms) in ED analysis. 

1) How do I extract the mean-square displacement along a certain eigenvector?

2) How do I get rid of jumps across the box? I have played with trjconv -pbc 
(whole/nojump/inbox) with no success...



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