Hi,
On Tue, May 7, 2013 at 9:58 PM, 赵媛 <zhaoyuanchem.stu.xmu.edu.cn> wrote:
> trajin ../md_2ns.mdcrd 901 2000 1
> trajin ../md_4ns.mdcrd 1 500 1
> average try.rst rest
You probably want to add an 'rms' command in between your 'trajin'
commands and the 'average' command to remove rotation/translation of
your molecule. Otherwise this translation/rotation will be averaged in
as well.
> however, the try.rst I obtained is blank, and the other file I obtained is try.rst.-1,
This seems strange, particularly the negative integer suffix of the
second file name. This was generated with the above input? What
version of ptraj are you using? Did you try using cpptraj?
> in this file, it has 32861 lines, but half lines are zero,
This is normal for ptraj. The Amber restart file format can contain
velocities, but since ptraj does not have any velocity information it
writes zeros. If you use cpptraj, velocity info will only be written
to restarts if present in the input coordinates (e.g. in a combined
mdcrd/mdvel netcdf file or via the 'mdvel' keyword).
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 Wed May 08 2013 - 08:30:02 PDT
