VMD-L Mailing List

From: Felipe Merino (felipe.merino_at_mpi-dortmund.mpg.de)
Date: Mon Apr 03 2017 - 03:51:46 CDT

Hi Daniela,

I think you are a bit confused on what you want to calculate. You cannot
get an RMSD from a single point in space such as the COM of the protein.
You can of course measure how much the COM has drifted during the
simulation, but that is another type of analysis. measure rmsd will work
on selections not on vectors which is why you see the error you see. The
mass weight you see in the RMSD tool is to give weight to the
displacement of each atom in the mean square calculation.

I hope that helps

Felipe

On 03/04/17 09:58, Daniela Rivas wrote:
> Dear VMD users,
>
> I'd like to measure the RMSD of the center of mass of my protein in a
> trajectory, but I haven't found a way to do it. I tried using the
> "weight mass" in the trajectory RMSD tool, but it gives me the exact
> same result as without the weight.
>
> I also tried writing the following script, but it didn't work either.
> It kept giving me the error "measure rmsd: no atom selection". I guess
> it's because the center of mass is not an atom.
>
> set chainA_top_reference [atomselect top "protein resid 109 to 225"
> frame 0]
> set CoM1_reference [measure center $chainA_top_reference weight mass]
> set chainA_top_compare [atomselect top "protein resid 109 to 225"]
>
> set file1 [open Top_CofM_RMSD_300K.dat w]
> set num_steps [molinfo top get numframes]
>
> for {set frame 0} {$frame < $num_steps} {incr frame} {
> $chainA_top_compare frame $frame
> set CoM1_compare [measure center $chainA_top_compare weight mass]
> set RMSD [measure rmsd $CoM1_compare $CoM1_reference]
> puts $file1 "$frame $RMSD"
> }
>
> close $file1
>
> Does anyone know how to do this?
>
> Thanks in advance,
> Daniela.