VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Wed Aug 01 2018 - 03:39:39 CDT

Again the same problem.

You use

[measure rmsd $sela $selb]

it should be measure rmsf

Secondly - this is not how rmsf is calculated.

the simplest way to calculate the RMSF is

load your trajectory
make 1 selection (just 1) holding your atoms of interest. (eg. roi_atoms)

now use

measure rmsf $roi_atoms

if you use the above command all frames in your trajectory will be used to
calculate the rmsf.
if you want to limit them as I think you are trying to do (not exactly
sure) add frame numbers

so

measuer rmsf $roi_atoms 50 60

with the above command only frame 50 through 60 will be used.

keep in mind the difference in math between RMSD and RMSF.
RMSD is per frame -- so you get a trend
RMSF is per set of frames -- so you will get just 1 value (doesn't matter
if you use 50 frames or 5000).

check this page for more details:

https://www-s.ks.uiuc.edu/Research/vmd/vmd-1.9.1/ug/node136.html

On Wed, Aug 1, 2018 at 4:17 PM Sasthi Charan Mandal <sasthi.phys_at_gmail.com>
wrote:

> Oh I am sorry. It will be rmsf. So it would be very much helpful for me if
> you would provide me the tcl script. I have one script but using this
> script I could not get the expected result. Could you please check my
> script and let me know what is wrong here?
> The script is:
> set outDataFile [open rmsf.dat w]
> for {set r 491} {$r <= 512} {incr r} {
> set sela [atomselect top "resid $r"]
> set selb [atomselect top "resid $r"]
> $sela frame 0
> for {set f 0} {$f<=9990} {incr f} {
> $selb frame $f
> display update
> set val [measure rmsd $sela $selb]
> set resid $r
> puts $outDataFile "$resid $f $val"
> }
> }
> close $outDataFile
> return
> }
>
> On Wed, Aug 1, 2018 at 6:10 AM, Ashar Malik <asharjm_at_gmail.com> wrote:
>
>> The subject of the mail is asking for rmsf where as in the email you say
>> rmsd. So which one?
>>
>> Rmsd and rmsf can both be obtained using the "measure" command.
>>
>> Remember to remove translational and rotational effects from your system
>> prior to their use.
>>
>> Write back if this doesn't help and an example "script" can be provided.
>>
>> On Aug 1, 2018 00:06, "Sasthi Charan Mandal" <sasthi.phys_at_gmail.com>
>> wrote:
>>
>> I want to calculate the rmsd of each base pair of dna over a specified
>> time.. So if anyone have the script I will be thankful to you if you
>> provide me.
>> Thanks
>>
>>
>>
> 

-- 
Best,
/A