From: Brian Radak (bradak_at_anl.gov)
Date: Thu Jun 16 2016 - 14:11:29 CDT
Then the "problem" is almost certainly that the reference structure is
different for both RMSD calculations -- a common mistake for people new
to simulation.
I would rerun the script with /both/ DCD files; the resulting RMSD
should be more inline with what you expect.
On a related note: Depending on what you are hoping to learn here, you
may want to try a different reference structure. It is not particularly
surprising that an unequilibrated structure (frame 0) is very different
from one generated by MD. You will almost always get a small RMSD that
quickly rises to a large value and then levels out. Choosing a later
reference structure would be a good way to indicate that the system is
actually equilibrating to a new region of configuration space. For more
rigorous calculations you could also try using an average structure as
the reference or else a structure chosen from some kind of clustering
algorithm.
Cheers,
Brian
On 06/16/2016 02:02 PM, faride badalkhani wrote:
> Hi,
>
> I am using this script:
>
> set outfile [open rmsd.dat w];
> set nf [molinfo top get numframes]
> set frame0 [atomselect top "all not waters" frame 0]
> set sel [atomselect top "all not waters"]
> # rmsd calculation loop
> for {set i 1 } {$i < $nf } { incr i } {
> $sel frame $i
> $sel move [measure fit $sel $frame0]
> puts $outfile "[measure rmsd $sel $frame0]"
> }
> close $outfile
>
> Actually, I just continued the simulation from 10 to 15 ns, and
> plotted the RMSD for it.
>
> Regards,
> Farideh
>
>
> On Thu, Jun 16, 2016 at 11:21 PM, Brian Radak <bradak_at_anl.gov
> <mailto:bradak_at_anl.gov>> wrote:
>
> RMSD requires a reference structure -- most programs (I expect you
> are using VMD, for example) default to using the initial
> configuration. Did you inadvertently reset this between two
> calculations or did you repeat the calculation for the complete 15
> ns trajectory?
>
> HTH,
> Brian
>
>
> On 06/16/2016 12:42 PM, faride badalkhani wrote:
>> Dear NAMD experts,
>>
>> I have a question regarding step by step simulations. I performed
>> a NPT simulation for 10 ns and then plotted the RMSD. Then I
>> continued the simualtion for 5 more ns. When I plot the RMSD for
>> 15 ns the plot is decreasing decreased from 12.5 to 0.7 when it
>> goes from first simulation to the second one. So, Could you give
>> me a clue where did I make a mistake?
>>
>> I am sorry if it is a silly question. I am a beginner in this area.
>>
>> Regards,
>> Farideh
>
> --
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
>
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643 <tel:%28630%29%20252-8643>
> brian.radak_at_anl.gov <mailto:brian.radak_at_anl.gov>
>
>
-- Brian Radak Postdoctoral Appointee Leadership Computing Facility Argonne National Laboratory 9700 South Cass Avenue, Bldg. 240 Argonne, IL 60439-4854 (630) 252-8643 brian.radak_at_anl.gov
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