[gmx-users] g_rms g_dipole

David spoel at xray.bmc.uu.se
Thu Nov 20 08:10:01 CET 2003

On Wed, 2003-11-19 at 22:09, parinald at unsl.edu.ar wrote:
> Hello gmx´ers:
>               I done MD for CL- and NA+ in water.
> g_rms compares two estructures by computing RMSD, now I get two curves 
> CL- and NA+, but I dont know how to reed that:
> are relative position?
> are related with size of the simulation box?
this is meaningless for ions. you are computing the difference in
> The file aver.xvg (of g_dipole) contains <|M|^2> and <|M|>^2, what the 
> meaning of <|M|>^2 / <|M|^2> ? what is N?.

>                                           Thank you. Pablo.
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David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel

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