VMD-L Mailing List

From: Andrew Jewett (jewett.ai_at_gmail.com)
Date: Tue Mar 06 2012 - 20:31:31 CST

I've no idea if you can do it from inside VMD, but once you have the
two molecules superimposed in VMD, you can save the coordinates of the
two structures (I recommend using XYZ format), paste them together
into a single file, (using unix "paste" command), and then compute the
x, y, or z component of the RMSD directly using awk.

The commands would be something like:

paste -d' ' file1.xyz file2.xyz | tail -n +3 > file12.dat
awk '{if (NF==8) {n++; sumsq+=($2-$6)^2}} END{print(sqrt(sumsq/n))}' <
file12.dat

(I'm guessing this gives you the RMSD in the X component. For the Y
and Z components, try sumsq+=($3-$7)^2, and sumsq+=($4-$8)^2)

I hope this helps.
Cheers

Andrew

On Tue, Mar 6, 2012 at 9:36 AM, patrick wintrode <pat_wde2_at_yahoo.com> wrote:
>
> Hi all.
>
> Is there a way to write out the x, y and z components of RMSD or RMSF
> separately in VMD?
>
> Thanks.
>
> Patrick L. Wintrode
> Associate Professor
> Dept. of Pharmaceutical Sciences
> University of Maryland School of Pharmacy