VMD-L Mailing List

From: Roni Saiba (ronis_at_imsc.res.in)
Date: Mon Jun 13 2022 - 02:06:32 CDT

I think your script is missing the alignment step prior to doing the
calculation. You can use the measure fit and moveby command to align
the trajectory to a reference of your choice. After the alignment is
complete you can measure the RMSD.
Regards,
Roni

Quoting Leonardo Palmieri <leopalmieri1_at_gmail.com>:

> Hi
>
> I'm using Calc. RMSD function of Timeline plugin to analyze
> trajectories. If I use it from the VMD GUI, results seems correct.
> But, if I use it in a script, for eg., the script proposed in titin
> Timeline tutorial "titin-per-res-rmsd.tcl" to generate a .tml file, I
> can't get the same results.
>
> RMSD values for some residues in some frames increases too much, not
> corresponding to what is happening in the molecule trajectory.
>
> The calculation part of the script that I'm using is the same from
> tutorial "titin-per-res-rmsd.tcl":
>
> ::timeline::writeDataFileHeader $outDataFile $molid $dataTitle $numFrames \
> $numSelectionGroups $usesFreeSelection
>
> set chain $theChain
> set seg $theSeg
> for {set r $firstRes} {$r <= $lastRes} {incr r} {
> set sela [atomselect $molid "resid $r"]
> set selb [atomselect $molid "resid $r"]
> $sela frame 0
> for {set f $firstFrame} {$f<=$lastFrame} {incr f} {
> $selb frame $f
> display update
> set val [measure rmsd $sela $selb]
> set resid $r
> puts $outDataFile "$resid $chain $seg $f $val"
> }
>
>
> eg of RMSD values:
>
> with GUI:
>
> 95 CYS frame 211: 6.64
> 95 CYS frame 212: 6.845
>
> with script:
>
> 95 CYS frame 211: 8.54
> 95 CYS frame 212: 20.75
>
> Is there something wrong with my script? Did I miss something?
>
> Thanks in advance!
>
>
>
> --
> att
>
> Leonardo Palmieri
>
> Pai de gente
> Pai de planta