Hi,
First of all keep in mind that the pseudo-trajectory you've created by
concatenating your individual umbrellas together is not necessarily a
real pathway, so the fact that the transition appears to occur in
steps could just be an artifact of the umbrella restraints. To see
actual pathways you'd have to do something like transition path
sampling.
To accomplish the clustering you want in cpptraj, you would first
RMS-fit chain A prior to the 'cluster' command, then cluster on chain
B with the 'nofit' keyword. See the manual for full details.
-Dan
On Wed, Apr 5, 2017 at 5:26 AM, d00b46022 <d00b46022.ntu.edu.tw> wrote:
> Dear all,
>
> A trajectory of umbrella sampling MD simulation for protein-peptide
> complex separation (chains A and B) is ready with me.From visual
> observation, i.e. extracted frames from the trajectory and aligned them
> and make a movie along time, can view nice separation. However, I am
> interested to perform cluster analysis over the trajectory to see
> whether the biased translation of peptide follow some specific path or
> not. The visual observation tells me that the translation happens in
> steps. Therefore, I wish to check whether the cluster analysis also show
> the same in term of more frame in clusters near these steps.
> I am going through basic cluster command in CPPTRAJ, however, I am not
> sure how to design.
> I want to keep the chain A fixed and wish to see the clusters for
> peptide chain B only.
>
> Any input in this regard would be great help.
>
> Thanking you in advance.
>
> -- Josh
>
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Apr 05 2017 - 10:30:03 PDT
