Changes between Version 3 and Version 4 of FittingPotentials

Timestamp:

Apr 15, 2015, 11:52:34 AM (10 years ago)

Author:

FrederikHeber

Comment:

finalized this application example

FittingPotentials

@@ -52 +52 @@
 Fitting single potentials is sensible if you create snapshots that only oscillate in the degrees of freedom of this single potential, e.g. if only an elongation of the oxygen-hydrogen bond has been excited and the angle between the two O-H bonds does not change. However, as we have created a molecular dynamics simulation of an unknown initial configuration, we cannot ascertain that such a precondition holds. This is also the reason why ''take-best-of'' has been specified and not ''set-threshold'' as you will probably have noticed that the remaining L2 error is still quite large.
 
-A compound potential is defined by a file of the following form (we use the '''.potentials''' format use by the [http://www.tremolo-x.com/ tremolo] package.
+A compound potential is defined by the file '''water.potentials''' (we use the '''.potentials''' format use by the [http://www.tremolo-x.com/ tremolo] package), see the attached file. You can either create such a file from scratch (the format is quite simple) or you can use the above ''fit-potential'' calls followed by a ''save-potentials'' action to store the fitted potential to a potentials file. Afterwards you can simply combine multiple potential files into a single one.
+
+Finally, we are able to fit the compound potential.
 {{{
+./molecuilder \
+        --parse-homologies homologies.dat \
+        --parse-potentials water.potentials \
+        --fit-compound-potential \
+                --fragment-charges 8 1 1 \
+                --take-best-of 3 \
+                --training-file training.dat \
+        --save-potentials water_final.potentials
+}}}
 
-}}}
+Note that the fitting of a compound potential will take longer than for a single potential as there are more degrees of freedom to consider: Each parameter of each potential represents one degree of freedom. Also note that the fit may fail if no sensible default value for each parameter is specified. If it fails, it is recommended to play around with the parameters a bit. Note that increasing verbosity (''--verbose 2'') will give you more information on how the iterative fitting procedure progresses.
+
+After a minute or so, the iteration will have stopped and in the file '''water_final.potentials''' the resulting potential parameters are given. Note that the contents of the file is also printed to the screen on default verbosity including information on remaining L2 error and so on.