Dear Daniel and Wei
Thanks, but I am lost somewhat I think...
1) rms using nofit means it will NOT transform/translate and use simply formula as in wiki RMSD (v,w): http://en.wikipedia.org/wiki/Root-mean-square_deviation_of_atomic_positions
2) rms without nofit will perform transform/translate to get best fit (which is best minimum rmsd out of all transformations)
am I right?
Then in that case I would like to check if internal geometry was fixed (for 1-10) using EMAPs then I should get flat rmsd for 1-10 residue for whole simulation just by using:
rms reference mass :1-10 out test.rms (as this should transformation to provide best fit)
thanks
On Tuesday, January 21, 2014 12:49 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
On Mon, Jan 20, 2014 at 4:46 PM, Jio M <jiomm.yahoo.com> wrote:
>
> rms reference mass :1-10 out test_fit.rms fit
>
FYI 'fit' is not a valid keyword for the 'rms' command in either ptraj or
cpptraj. As Wei mentioned the default behavior of 'rms' in both programs is
to calculate the best-fit RMSD. The 'nofit' keyword means do not perform
any fitting; the RMSD is calculated between the target and reference
structures as they are.
-Dan
--
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
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 Mon Jan 20 2014 - 18:00:02 PST
