VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Feb 02 2017 - 11:03:32 CST

Hi Dmitry,

It depends on what you mean by correct. The measure rmsf command does no
prefitting on its own, and will calculate the reference structure from
the average of the current frames. What I normally do is align my
trajectory to a suitable reference (the original pdb or frame 0) and
then ask for the RMSF, since the value tends to be smaller than if you
didn't remove the normal diffusional drift from your simulations first.

-Josh

On 02/02/2017 06:08 AM, Dmitry Suplatov wrote:
> 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
>>
>>
>
>