Dear Daniel,
Thank you so much!
Best Regards,
Hocine
El 6 feb 2023, 14:43 +0100, Daniel Roe <daniel.r.roe.gmail.com>, escribió:
> Hi,
>
> Yes, you can use the 'filter' command and/or the 'outtraj' command
> with the 'maxmin' keyword to extract frames based on specific dataset
> values. Of course, you need to ensure that the trajectory you are
> extracting frames from is the same one used to generate the covariance
> matrix you used. So something like this:
>
> # Step 1: Read in previously calculated PCs.
> # I'm assuming PC1 in column 2 and PC2 in column 3
> readdata pca12.dat name MyPcProjection
> # Step 1: Fit trajectory frames.
> parm complex.psf
> trajin complex.dcd
> trajin complex.dcd
> trajincomplex.dcd
> rms first .CA
> average crdset avg_set
> createcrd traj_set
> run
> crdaction traj_set rms ref avg_set @CA
> # Step 2: Use maxmin to separate frames by bin values in MyPcProjection.
> # MyPcProjection:2 should be PC1 from column 2.
> crdaction traj_set outtraj Bin1.dcd maxmin MyPcProjection:2 min
> <min1-1> max <max1-1> maxmin MyPcProjection:3 min <min1-2> max
> <max1-2>
> ...
>
> Here <minX-Y> and <maxX-Y> are the minimum and maximum values for
> defining bin X, principal component projection Y. You can do an
> 'outtraj' command for each bin of interest. Now keep in mind the
> frames extracted in such a manner are "representative" only insofar as
> they come from that bin.
>
> To make things more efficient in the future (and assuming disk space
> is not an issue), it may be worth it to save the fit trajectory (i.e.
> the trajectory you use to calculate the covariance matrix and do
> projections) to a separate file so you don't have to keep regenerating
> it on the fly.
>
> Hope this helps,
>
> -Dan
>
> On Fri, Feb 3, 2023 at 4:46 AM Hocine EL KHAOUDI ENYOURY via AMBER
> <amber.ambermd.org> wrote:
> > parm complex.psf
> > trajin complex.dcd
> > trajin complex.dcd
> > trajincomplex.dcd
> >
> > rms first @CA
> > average crdset avg_set
> >
> > createcrd traj_set
> >
> > run
> >
> > crdaction traj_set rms ref avg_set @CA
> >
> > crdaction traj_set matrix covar :.CA name pro_covar out covmat.dat
> >
> > runanalysis diagmatrix pro_covar out evecs.dat vecs 100 name myevecs nmwiz nmwizvecs 100 nmwizfile complex.nmd nmwizmask :@CA
> > runanalysis modes eigenval name myevecs out evalfrac.dat
> > runanalysis modes fluct out rmsfluct1-10.dat name
> > myevecs beg 1 end 10 #to write the fluctuations of first 10 PCs
> >
> > runanalysis modes fluct out rmsfluct1-2.dat name myevecs beg 1 end 2
> >
> > runanalysis modes fluct out rmsfluct-mode1.dat name myevecs beg 1 #to write the fluctuations of first PC
> >
> > crdaction traj_set projection p1 modes myevecs beg 1 end 20 @CA out pca.dat #to write the projections
> > of first 20 PCs
> >
> > crdaction traj_set projection p2 modes myevecs beg 1 end 2 :@CA out pca12.dat #to write the projections of first 2
> > PCs
> >
> > runanalysis hist p1:1 p1:2 bins 100 free 300 out fhist-all.CA.agr
> >
> > Is there a way to extract a representative structure of each bin of the plot?
> >
> >
> > Thanks!
> >
> > Hocine
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 06 2023 - 06:00:04 PST
