Hi,
It's not clear to me that RMSD is a useful metric for a single atom.
You may want to look at something like 'diffusion' instead.
-Dan
On Wed, Mar 23, 2016 at 10:25 PM, Francesco Gentile
<fgentile.ualberta.ca> wrote:
> Hello,
> I run 100 ns of MD simulations of a protein containing a coordinated
> divalent metal ion. When calculating the RMSD, I obtain a value of 0
> angstroms for the ion, during the whole trajectory. I visualized the
> trajectory and the ion is fluctuating. here it is the script I am using for
> cpptraj
>
> trajin ...
> center :1-132 mass origin
> image origin center familiar
> rms first mass out rms_back_bgw.dat ':1-132.CA,C,N' time 2.0
> rms first mass out rms_mg_bgw.dat ':133.MG' time 2.0
>
> where residue 1-132 is the protein and 133 is the ion. I also tried to
> calculate the ion alone
>
> trajin ...
> center :133 mass origin
> image origin center familiar
> rms first mass out rms_mg_bgw.dat ':133.MG' time 2.0
>
> but still the output is 0 for all the snapshots. Could you suggest me
> possible reasons for this strange behaviour? Thanks in advance
>
> --
> Francesco Gentile
> PhD Student, Biophysics
> CCIS 3-215, Department of Physics
> 7-112, Li Ka Shing Centre for Health Research Innovation
> University of Alberta, Edmonton, AB T6G 2E1
> Canada
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Mar 24 2016 - 09:30:09 PDT
