Hi Daniel
Sorry looks like I messed up everything. Actually I want to do similar
analysis done with gromacs '' filter the trajectory to show only the motion
along eigenvectors"
I am not sure how this can be implemented here. I modified last part as:
readdata evecs.dat
crdaction crd1 projection modes evecs.dat out myproj.txt beg 1 end 1
:1-382.N
readdata myproj.txt
filter myproj.txt min -10 max 10 out filter.dat
trajout filter.nc
So if it is to be motion along eigenvector 1 then I should choose max and
min values (Mode1) from myproj.txt ?
Also one more thing does pseudo-trajectory (from 'modes trajout') means an
interpolation between two extremes?
thanks
On Sat, Jun 21, 2014 at 9:48 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Sat, Jun 21, 2014 at 11:07 AM, newamber list <newamberlist.gmail.com>
> wrote:
>
> > crdaction crd1 projection modes evecs.dat out myproj.txt beg 1 end 8
> > :1-382.N
> > modes trajout filter_1.nc trajoutfmt netcdf name test pcmin -100 pcmax
> 100
> > tmode 1
> >
> > I have following problems/queries:
> >
> > 1) I always get 201 frames. I am not sure why is it so? No matter how
> many
> > frames are there in trajin and which mode I trajout, its always 201.
> >
>
> Note that for the 'modes' analysis, 'trajout' is a keyword requesting
> generation of a pseudo-trajectory along a specified eigenvector. In this
> case you are requesting that the 'modes' analysis create a psuedo
> trajectory along your first eigenvector ranging from a projection value of
> -100 to 100; (100 - -100 + 1) = 201 frames. You should also ensure that the
> minimum and maximum projection values are reasonable (by e.g. creating a
> histogram of the projection values from your input trajectories).
>
>
> >
> > 2) Also how I can get frame number from input trajectory (trajin) which
> are
> > filtered out and saved in some output trajectory (modes trajout)
> >
>
> It's not clear from your description what exactly you are trying to filter.
> Do you want frames that fall within certain principal component projection
> values? If so you need to use the 'filter' action on the data set(s) you
> get from the 'projection' action, followed by a 'trajout' command.
>
>
> >
> > 3) Also please let me know if I understood it correctly: If am not wrong
> > then the filtered trajectory so obtained should contain the extreme
> > projections? Thus the two extreme projections should 'reflect' the filter
> > trajectory in summary.
> >
>
> I'm not sure I understand this question completely, but the first and last
> frames of your pseudo-trajectory (from 'modes trajout ...') will correspond
> to projection values <pcmin> and <pcmax> along the specified eigenvector.
>
> Hope this helps,
>
> -Dan
>
>
> >
> > Thanks for any help
> >
> > regards
> > JIom
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> 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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>
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Received on Sat Jun 21 2014 - 19:00:02 PDT
