Re: [AMBER] Separating a trajectory by output from clusterdihedral

From: Daniel Roe via AMBER <amber.ambermd.org>
Date: Sun, 23 Apr 2023 15:11:10 -0400

Hi,'

You could use the 'outtraj' action with the 'maxmin' keyword to
extract frames of a specific cluster number from the cluster # vs time
data set. For example,

readdata clustervtime.dat name CVT
parm myparm.parm7
trajin mytraj.nc
outtraj cluster1.nc maxmin CVT min .5 max 1.5
outtraj cluster2.nc maxmin CVT min 1.5 max 2.5

etc for each cluster you want to extract. I haven't tested this but
this (or something similar) should work I think.

 Hope this helps,

-Dan

On Sun, Apr 23, 2023 at 1:38 PM Osman, Roman via AMBER
<amber.ambermd.org> wrote:
>
> Hello,
>
> I would like to separate a trajectory by the clusters produced by clusterdihedral.
> I have two dihedrals that cluster into two clusters with nearly equal populations because their changes are correlated.
> In the out file from cpptraj I get a list of frames that belong to each cluster, but because the trajectory has 50000 snapshots the list is quite long (~25,000 entries).
> The question is whether I can use this list to write the trajectory with onlyframes and supply this long list.
>
> Or perhaps is another way to cluster the trajectory by the dihedrals and write the two clusters separately.
>
> Thanks for your help.
>
> Roman Osman
> Professor
> Department of Pharmacological Sciences
> Icahn School of Medicine at Mount Sinai
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

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Received on Sun Apr 23 2023 - 12:30:02 PDT
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