From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Thu Jun 16 2016 - 14:02:43 CDT
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
> brian.radak_at_anl.gov
>
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