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Commit 598e9275 authored by carlocamilloni's avatar carlocamilloni
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isdb-2 tutorial: make it more 'robust'

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......@@ -34,7 +34,7 @@ Given a PDB file, PLUMED is able to compute SAXS intensities for the molecule in
While computing scattering intensities with a full atomistic representation is quite easy (see the \ref SAXS keyword and later in this tutorial), in order to adopt the hybrid coarse-grained/atomistic approach a more elaborated procedure is needed, requiring the generation of few specific files to be used as input by \ref driver. To facilitate this step, it is possible to use this script (martiniFormFactor_p2.py for python 2 or martiniFormFactor_p3.py for python 3) and type in the bash shell:
\verbatim
python martiniFormFactor_p3.py -f filepdb.pdb -dat filedat.dat [-unit Ang/nm -nq 15]
python martiniFormFactor_p3.py -f start.pdb -dat SASDAB7.dat [-unit Ang/nm -nq 15]
\endverbatim
The input files are:
......@@ -49,11 +49,11 @@ The files generated in this step, to be used later as input for \ref driver, are
The default files generated should be sufficient to post-process single PDB files or trajectories, by typing:
\verbatim
plumed driver --plumed plumed.dat --mf_pdb file.pdb
plumed driver --plumed plumed.dat --mf_pdb start.pdb
\endverbatim
or
\verbatim
plumed driver --plumed plumed.dat --mf_xtc file.xtc
plumed driver --plumed plumed.dat --mf_xtc samplextc.xtc
\endverbatim
The output files generated by this step are:
......
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