Hi,
First, have you visualized the imaged trajectory to see if your issue
is actually due to imaging artifacts? In order to do this you will
need a much simpler script. Also, it's tough to tell because your
ptraj script as you posted it is jumbled (no newlines) but the
'trajout' command does not accept a mask (i.e. the '.N1,C' does
nothing). To make things simpler just 'trajin' a small portion of
xxx.mdcrd where the RMSD jumps occur so you can see what is going on.
For example, if one of the jumps occurs within the first 50 frames:
trajin ./xxx.mdcrd 1 50 1
center :1-677 origin
image origin center familiar
trajout imaged.netcdf netcdf
Also, is your protein (residues 1-677) a monomer?
-Dan
On Tue, Jul 17, 2012 at 9:18 PM, Catein Catherine
<askamber23.hotmail.com> wrote:
>
> Dear Sir/Madam,
> I have done a long simulation. In order not to avoid the problem of outside box, I have used iwrap=1, in all my calculations.
> According to the previous comments I added the "center and image origin" to the ptraj run (1-677 represent all the protein 677 protein residues)
> trajin ./xxx.mdcrdcenter :1-677 originimage origin center familiartrajout yyy.netcdf netcdf .N1,CAradgyr out yyy_all.radgyr.datrms first out xxx_all.rms .CA,C1
> atomicfluct out xxx.bfactor byres bfactoratomicfluct out xxx.nobfactor .CA,C1 byresaverage xxx_average_nobox.pdb pdb noboxmatrix correl .CA,C1 out xxx.corr byreshbond distance 3.5 angle 120.0 solventdonor WAT O solventacceptor WAT O H1 solventacceptor WAT O H2 out xxx.WAT.hbond2
> I found the profile is still strange. e.g the rmsd jump up and down to a very large values. It seems that when the molecule is moved to fit the box size, it affect all the analyzing parameters.
> Please kindly instruct if I have using the ptraj commands wrongly. Many thanks.
> Many thanks.
> Cat
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Lab Specialist
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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 18 2012 - 07:30:02 PDT
