From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Thu Jun 16 2016 - 14:13:40 CDT
Thank you so much!
Regards,
Farideh
On 16 Jun 2016 15:11, "Brian Radak" <bradak_at_anl.gov> wrote:
> 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> 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 <%28630%29%20252-8643>
>> 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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