VMD-L Mailing List

From: Dmitry Suplatov (genesup_at_gmail.com)
Date: Thu Feb 02 2017 - 05:59:35 CST

Since nobody replied to my question I will reformulate it.

I want to calculate RMSF of a residue within [k; n] timeframe of my
trajectory.

Question: Do I need to run some kind of preprocessing of my trajectory
before running the "set rmsf [measure rmsf $selection first $first last
$last]" command? By preprocessing I mean, e.g., backbone best-fit of all
frames in a trajectory, etc. Can I simply load the trajectory and run
the "measure rmsf" command straight away to get the correct results?

Thank you for your time.

Best,

Dmitry

On 01/31/2017 08:32 PM, Dmitry Suplatov wrote:
> Hello,
>
> I want to calculate RMSF of a specific residue. I want the reference
> structure to be updates every n frames.
>
> The basic command for calculating RMSF in VMD is:
>
> set rmsf [measure rmsf $selection first $first last $last]
>
> QUESTIONS:
>
> 1/ Do I understand correctly the the "measure rmsf" command will
> automatically calculate an average structure of my $selection within
> [$fist; $last] timeframe and then use it as reference for RMSF
> calculations?
>
> 2/ If the answer to 1/ is Yes, then I can achieve my goal (update the
> reference structure every $n frames) by running a loop
>
> for {set k $first} {$k<=[expr {$last-$step}] } {incr k $n} {
>
> set rmsf [measure rmsf $selection first $k last [expr {$k+$n}]]
>
> }
>
> ?
>
> Thank you for your time
>
> Dmitry
>
>