[gmx-users] Differences in the values of RMSD
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
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
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
More information about the gromacs.org_gmx-users