Hi,
You want to create a 2 dimensional histogram of the projection data
along whichever eigenvectors you choose, e.g. (assuming
dih.project.dat contains your projection data in columns, with column
1 being the frame #, column 2 being the projection along the 1st
eigenvector, etc):
readdata dih.project.dat name Project
runanalysis hist Project:2 Project:3 name bins 100 out project.ev.1.2.gnu
This will write the 2d histogram in gnuplot format. *If* you are
certain you have converged data (and that is a very important "if")
you can add the 'free <temperature>' keyword to calculate
population-based free energy values for each bin at the specified
temperature.
If you haven't seen this tutorial already you may find it helpful:
https://amberhub.chpc.utah.edu/introduction-to-principal-component-analysis/
Hope this helps,
-Dan
On Tue, Jul 19, 2022 at 11:24 PM ning via AMBER <amber.ambermd.org> wrote:
>
> Hi, Amber community
>
>
> I tried to make a free energy landscape (FEL) about protein conformation changes during accelerated MD simulation. However, when trying the tutorial guidance (https://ambermd.org/tutorials/advanced/tutorial22/section3.php), some strange errors appeared. I don't know what happen about the version upgrade from amber14 to amber20. Anyway, I decided to use another way, such as dihedral angle method, to get the FEL plotting. Here is my cpptraj input commands:
>
>
> Here is part1:
> parm s.prmtop
> trajin s_prod_amd1.nc
> multidihedral BB phi psi resrange 1-58 out PhiPsi_1-58.dat
> run
> matrix dihcovar dihedrals BB[*] out dihcovar.dat name DIH
> diagmatrix DIH vecs 6 out modes.dihcovar.dat name DIHMODES
> run
>
>
> Here is part2:
> parm s.prmtop
> trajin s_prod_amd1.nc
> readdata PhiPsi_1-58.dat name BB
> dataset mode torsion BB
> readdata modes.dihcovar.dat name MyModes
> projection evecs modes MyModes out dih.project.dat beg 1 end 6 dihedrals BB
> run
>
>
> When it finished, I got these files: PhiPsi_1-58.dat, modes.dihcovar.dat, dihcovar.dat, dih.project.dat. Now, how do I convert the dih.project.dat into a dataset for FEL plotting using cpptraj or other programs? If some errors appeared in my commands, please remind me, thanks!
>
>
> Sincerely,
> Ning
>
>
>
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Received on Thu Aug 04 2022 - 13:35:26 PDT
