Hello,
an 'rmsd' action by default first performs a structural alignment
between two selections and then measures the distance. The alignment
performed is 'sticky', it also takes effect for all subsequent commands
in a (cp)ptraj run. What you want is possible by the combination of two
'rmsd' commands, the first performing the alignment using a certain
selection of atoms, and the second one performing only the measurement
on a different selection of atoms. The latter works with the 'nofit'
argument within an 'rmsd' command which skips alignment before
measuring. Hence, use something like this in your input file:
# Align maskA in all frames to maskA in first frame.
# (Use rmsd command for that, but don't define output)
rmsd maskA first
# Measure distance of maskB in first frame to maskB in all frames
# without performing any structural alignment. Define an output
# data set.
rmsd maskB first nofit out distance.dat
Note that I have only tested this in cpptraj (which you also might want
to use, especially when dealing with NetCDF trajectories).
Cheers,
Jan-Philip
On 08/15/2013 04:34 AM, moitrayee.mbu.iisc.ernet.in wrote:
> Dear All,
> I want to do the following for an oligomer.
>
> I want to superimpose each snapshot on 1 subunit and calculate time dependent
> RMSD in the two neighboring subunits. Is there a way I can use ptraj to do this
> ?
>
> I would eagerly look forward to your reply.
>
> Thanks a lot and Best Regards,
> Moitrayee
>
>
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Received on Thu Aug 15 2013 - 01:30:06 PDT
