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Martin Kurečka
Plumed AlphaFold
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11e828df
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11e828df
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7 years ago
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Gareth Tribello
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Added some documentation to new INENVELOPE command
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CHANGES/v2.4.txt
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CHANGES/v2.4.txt
src/multicolvar/VolumeBetweenContours.cpp
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src/multicolvar/VolumeBetweenContours.cpp
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CHANGES/v2.4.txt
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@@ -21,6 +21,8 @@ Changes from version 2.3 which are relevant for users:
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@@ -21,6 +21,8 @@ Changes from version 2.3 which are relevant for users:
- \ref EDS
- \ref EDS
- New collective variables:
- New collective variables:
- \ref DIMER (thanks to Marco Nava).
- \ref DIMER (thanks to Marco Nava).
- New actions:
- \ref INENVELOPE
- Other changes:
- Other changes:
- \ref PBMETAD : multiple walkers using files (thanks to Marco De La Pierre).
- \ref PBMETAD : multiple walkers using files (thanks to Marco De La Pierre).
- \ref PBMETAD : adaptive gaussians
- \ref PBMETAD : adaptive gaussians
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This quantity can be used to calculate functions of the distribution of collective
This quantity can be used to calculate functions of the distribution of collective
variables for the atoms that lie in a region where the density of a certain type of atom is high.
variables for the atoms that lie in a region where the density of a certain type of atom is high.
This collective variable can be used to determine whether colvars are within region where the density
of a particular atom is high. This is achieved by calculating the following function at the point where
the atom is located \f$(x,y,z)\f$:
\f[
w_j = 1 - \sigma\left[ \sum_{i=1}^N K\left( \frac{x-x_i}{\sigma_x},\frac{y-y_i}{\sigma_y},\frac{z-z_i}{\sigma_z} \right) \right]
\f]
Here \f$\sigma\f$ is a \ref switchingfunction and \f$K\f$ is a \ref kernelfunctions. The sum runs over the atoms
specified using the ATOMS keyword and a \f$w_j\f$ value is calculated for each of the central atoms of the input
multicolvar.
\par Examples
\par Examples
The input below calculates a density field from the positions of atoms 1-14400. The number of the atoms
that are specified in the DENSITY action that are within a region where the density field is greater than
2.0 is then calculated.
\verbatim
d1: DENSITY SPECIES=14401-74134:3 LOWMEM
fi: INENVELOPE DATA=d1 ATOMS=1-14400 CONTOUR={RATIONAL D_0=2.0 R_0=1.0} BANDWIDTH=0.1,0.1,0.1 LOWMEM
PRINT ARG=fi,rr.* FILE=colvar
\endverbatim
*/
*/
//+ENDPLUMEDOC
//+ENDPLUMEDOC
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