Hi Daniel
Thanks for explained reply. Also it will be nice to include such option in
cpptraj in future.
best regards
On Tue, Jun 24, 2014 at 4:42 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Sat, Jun 21, 2014 at 7:34 PM, newamber list <newamberlist.gmail.com>
> wrote:
>
> > 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"
> >
>
> If I understand the purpose of this functionality correctly, this is not
> currently implemented in cpptraj. You can only obtain the projection of
> coordinates along specified eigenvectors (the 'projection' action).
>
>
> > 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 ?
> >
>
> First, you don't need to read myproj.txt back in - in fact during
> processing it will not have been generated yet so this statement should be
> removed. You can then give the projection data set a name in the
> 'projection' action (e.g. "myprojection") and refer to it that way, like
> so:
>
> readdata evecs.dat
> crdaction crd1 projection myprojection modes evecs.dat out myproj.txt beg 1
> end 1 :1-382.N
> filter myprojection:1 min -10 max 10 out filter.dat
> trajout filter.ev1.nc
>
> This will give you all frames with projection values between -10 and 10 for
> the first eigenvector. Note that I am using a data set index (":X") in the
> 'filter' command; in this case since you are only generating one projection
> it is unnecessary, but if you have more than one projection this will
> select the one you want (1 for projection along eigenvector 1, 2 for
> eigenvector 2, etc).
>
> Note that the frames will contain contributions from other modes as well.
> You could try to filter some of them out with additional filter commands,
> like so:
>
> crdaction crd1 projection myprojection modes evecs.dat out myproj.txt beg 1
> end 10 :1-382.N
> filter myprojection:1 min -10 max 10 out filter.dat
> filter myprojection:2 min -1 max 1 out filter.dat
> filter myprojection:3 min -1 max 1 out filter.dat
>
> etc. However, you may not have a lot of frames that fit this criteria so it
> may not work so well.
>
> Also one more thing does pseudo-trajectory (from 'modes trajout') means an
> > interpolation between two extremes?
> >
>
> What the pseudo-trajectory option does is take the average structure
> (generated during the matrix creation step and stored in your evecs output
> file) and project it along a specified mode with respect to the minimum and
> maximum projection values you specify. So in that sense it is an
> interpolation between specified extremes.
>
> Hope this helps,
>
> -Dan
>
>
> >
> >
> > 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
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > 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)
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
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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)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jun 24 2014 - 18:00:02 PDT
