[gmx-users] Differences in the values of RMSD

David spoel at xray.bmc.uu.se
Sat May 14 21:43:36 CEST 2005

On Sat, 2005-05-14 at 14:43 -0300, Jair wrote:
> I'm trying to calculate the rmsd values using g_rms, but small values are 
> produced as compared to VMD values.
> I used g_rms in the following way:
> g_rms -s prot.tpr -f prot_md.trr -o rmsd.xvg
> where the prot.tpr file is the file generated by grompp for the md simulation
> I selected Group 4 (Backbone), then
> I selected just one group to compare
> I selected Group 4 again to do the calculation
> RMSD values grows from zero to approximatelly 0.3nm after 5ns of simulation. 
> The values of RMSD analyzed with VMD  are between 1.5 nm and of 2.3 nm
> They are very different. Where is my mistake?
Vmd gives you Ångström I presume.

> Thanks for any suggestion
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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://xray.bmc.uu.se/~spoel

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