Hi,
You will need to modify your original cpptraj script for generating
PCs somewhat.
On Mon, Mar 9, 2015 at 3:14 AM, abdennour braka
<abdennour.braka.univ-orleans.fr> wrote:
> parm prot_OBC.top
> trajin 1_replic_traj.trj
> reference min.rst
> rms reference
>
> matrix covar name matrixdat .CA out covmat-ca.dat
> analyze matrix matrixdat out evecs-ca.dat vecs 174
> analyze matrix matrixdat name evecs-ca vecs 174
You don't need two 'analyze matrix' commands here, just one will do
(and 'diagmatrix' is the preferred name for this analysis now):
diagmatrix matrixdat name evecs-ca out evecs-ca.dat vecs 174
> analyze modes fluct out analyzemodesflu.dat name evecs-ca beg 1 end 174
> analyze modes displ out analyzemodesdis.dat name evecs-ca beg 1 end 174
Your 'run' command should come here, *before* you attempt your
projection calculation since at this point nothing has been
calculated. So the next two commands should be:
run
projection evecs evecs-ca out pca12-ca.dat beg 1 end 3 .CA
Does that make sense to you? Let me know if not.
As far as creating a weighted histogram, cpptraj can do this as well
given that you have your boost energies in KT. Assuming you have them
in a file called e.g. amdboost.dat in a single column, you could read
that and your previously-calculated PC projections and calculate the
reweighted 2D histogram like so:
readdata amdboost.dat name BOOST
readdata pca12-ca.dat name PC
runanalysis hist PC:2 PC:3 amdboost BOOST bins 200 free 300 out
hist.pca12-ca.gnu
The '2' and '3' for PC are used since pca12-ca.dat has data for the
first and second PC projections in columns 2 and 3. You can use 'list
dataset' after 'readdata' to see currently loaded data. Here no number
is needed for BOOST since there is only 1 column of data. The '.gnu'
extension will write the resulting histogram in gnuplot-readable
format.
Note that this kind of reweighting is very straightforward. There are
other ways to reweight aMD data out there that you may want to check
out, notably here:
http://mccammon.ucsd.edu/computing/amdReweighting/
Hope this helps,
-Dan
run
> ###########################################
> Thank you four any replies,
>
> Abdennour
> //
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Mon Mar 09 2015 - 07:30:07 PDT
