Re: [AMBER] filter trajectory with modes same number of frames

From: Daniel Roe <>
Date: Sat, 21 Jun 2014 14:48:33 -0600


On Sat, Jun 21, 2014 at 11:07 AM, newamber list <>

> crdaction crd1 projection modes evecs.dat out myproj.txt beg 1 end 8
> :1-382.N
> modes trajout 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,


> Thanks for any help
> regards
> JIom
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sat Jun 21 2014 - 14:00:03 PDT
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