On Mon, Jun 13, 2016 at 6:55 AM, Jean-Patrick Francoia
<jeanpatrick.francoia.gmail.com> wrote:
> I have about 20 coordinates files I load into cpptraj with the trajin
> command. Each file contains 1000 frames.
>
> I would like to perform a rmsd, something like:
>
>
> rms first mass out rms.agr
>
>
> However in this command, the first frame is used as the reference. How
> can I set, let's say, frame #1456 as the reference ?
Presumably overall frame 1456 is frame 456 of the second trajectory if
all trajectories contain 1000 frames. So do something like:
parm myparm.parm7
reference traj2.nc 456
trajin traj1.nc
trajin traj2.nc
...
trajin trajN.nc
rms reference mass out rms.agr
You may also want to check out the cpptraj RMSD tutorial:
http://ambermd.org/tutorials/analysis/tutorial1/
Hope this helps,
-Dan
>
>
> Best regards
>
>
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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 Mon Jun 13 2016 - 07:30:03 PDT
