VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Feb 13 2008 - 10:58:13 CST

Did you select "backbone", "trace", or "noh" in the RMSD tool? In your
script, you are looking at all the atoms, including hydrogens, but I would
guess you were not including them (by checking "noh") in the RMSD trajectory
tool calculation. That could explain the difference.

 

 

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Jorgen Simonsen
Sent: Wednesday, February 13, 2008 10:18 AM
To: vmd
Subject: vmd-l: rmsd different from rmsd implemented in VMD

 

Hi,

I get different results when I use the RMSD Trajectory tool and my script
below - both of them should align to a reference structure and then compute
the RMSD. The problem is that I get different numbers depending on which
method I use - I would expect them to be identical..

VMD Script
 0.310802847147 0.334529817104

Any help or comments appreciated
Thanks in advance

Best
J

        proc print_rmsd_through_time {{mol top}} {
                # use frame 0 for the reference
                set reference [atomselect $mol "protein" frame 0]
                # the frame being compared
                set compare [atomselect $mol "protein"]

                set num_steps [molinfo $mol get numframes]
                for {set frame 0} {$frame < $num_steps} {incr frame} {
                        # get the correct frame
                        $compare frame $frame

                        # compute the transformation
                        set trans_mat [measure fit $compare $reference]
                        # do the alignment
                        $compare move $trans_mat
                        # compute the RMSD
                        set rmsd [measure rmsd $compare $reference]
                        # print the RMSD
                        puts "RMSD of $frame is $rmsd"
                }
        }

print_rmsd_through_time