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Evelyne Deplazes
Umbrella-Integration
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b98b4485
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b98b4485
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Oct 24, 2016
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Evelyne Deplazes
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@@ -131,15 +131,15 @@ python umbrella_integration.py -i infile -o outfile -b binwidth
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@@ -131,15 +131,15 @@ python umbrella_integration.py -i infile -o outfile -b binwidth
-i infile
-i infile
name of input file, if file is not in the same directory as
name of input file, if file is not in the same directory as
the script, the full path needs to be given. (see below for details on
the script, the full path needs to be given. (see below for details on
the format of the input file).
the format of the input file).
-b bin_width
-b bin_width
the bin width used for 'binning derivatives' when calculating the PMF
the bin width used for 'binning derivatives' when calculating the PMF
(ie when combining the data from the different windows).
(ie when combining the data from the different windows).
if -b is not given, the default of 0.2 (nm) is used.
if -b is not given, the default of 0.2 (nm) is used.
This is independent of the spacing between umbrellas/windows used
This is independent of the spacing between umbrellas/windows used
in the umbrella sampling simulations.
in the umbrella sampling simulations.
NOTE: the bin widths affects the final PMF so this
NOTE: the bin widths affects the final PMF so this
should be carefully considered (see also Kästner & Thiel 2005).
should be carefully considered (see also Kästner & Thiel 2005).
Instead of the bin_width -n and -m can be used to provide
Instead of the bin_width -n and -m can be used to provide
the number of binds and the range (min,max) for the
the number of binds and the range (min,max) for the
...
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