Hi,
On Mon, Jul 16, 2012 at 7:25 AM, Catein Catherine
<askamber23.hotmail.com> wrote:
> However, when I do
> rms first out xxx_all.rms .CA,C1
>
> atomicfluct out xxx.bfactor byres bfactor
>
> I found the profile is very strange. Please kindly refer to my attached excel files for the profiles.
To show things like this it is probably better to either attach a JPG
(or similar) format plot or the raw XY data (at least for me since I
don't have MS office installed).
Does "strange" mean the RMS makes large jumps every now and then,
corresponding to imaging artifacts? If so you could update to the
latest version of AT12 (bugfix.16) which introduces a new command to
cpptraj, 'autoimage', which may do a better job imaging your
trajectory. To use, simply specify 'autoimage', e.g.:
trajin mdcrd
autoimage
trajout imaged.nc netcdf
Hope this helps,
-Dan
--
-------------------------
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) 585-9119 (Fax)
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Received on Thu Jul 26 2012 - 19:30:03 PDT
