VMD-L Mailing List

From: Dmitry Suplatov (genesup_at_gmail.com)
Date: Tue Jan 31 2017 - 11:32:04 CST

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