I.e. a single point can always align perfectly with itself.
Bill
On 3/23/16 9:30 PM, Hai Nguyen wrote:
> Hi,
>
> you used the best fit rmsd for ion, so getting 0. value is correct. You
> should add "nofit" keyword.
>
> 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 *notfit*
>
> You can check Jason' answer here:
> http://archive.ambermd.org/201108/0809.html
> (further:
> https://www.google.com/webhp?sourceid=chrome-instant&ion=1&espv=2&ie=UTF-8#q=cpptraj%20nofit
> )
>
> cheers
> Hai
>
> On Thu, Mar 24, 2016 at 12:25 AM, 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Wed Mar 23 2016 - 22:00:05 PDT
