Fwd: Re: [gmx-users] Differences in the values of RMSD

Jair jair at iq.ufrj.br
Mon May 16 14:58:22 CEST 2005

Of course, it was a really stupid question
 Iḿ sorry!

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.

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