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Martin Kurečka
Plumed AlphaFold
Commits
39aa2dac
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Commit
39aa2dac
authored
9 years ago
by
Giovanni Bussi
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CHANGES/Unreleased.txt
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user-doc/tutorials/moving.txt
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CHANGES/Unreleased.txt
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@@ -28,6 +28,7 @@ Changes from version 2.1 which are relevant for users:
...
@@ -28,6 +28,7 @@ Changes from version 2.1 which are relevant for users:
- \ref MFILTER_BETWEEN
- \ref MFILTER_BETWEEN
- \ref GRADIENT can be used to calculate the gradient of a quantity. Used to drive nucleation
- \ref GRADIENT can be used to calculate the gradient of a quantity. Used to drive nucleation
- \ref CAVITY
- \ref CAVITY
- \ref PUCKERING (thanks to Alejandro Gil-Ley).
- \ref WRAPAROUND to fix periodic boundary conditions.
- \ref WRAPAROUND to fix periodic boundary conditions.
- New features for existing actions:
- New features for existing actions:
- Keywords UPDATE_FROM and UPDATE_UNTIL to limit update step in a defined time window.
- Keywords UPDATE_FROM and UPDATE_UNTIL to limit update step in a defined time window.
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@@ -38,6 +39,7 @@ Changes from version 2.1 which are relevant for users:
...
@@ -38,6 +39,7 @@ Changes from version 2.1 which are relevant for users:
- \ref driver accepts a --mc flag to read charges and masses from a file produced during
- \ref driver accepts a --mc flag to read charges and masses from a file produced during
molecular dynamics with \ref DUMPMASSCHARGE
molecular dynamics with \ref DUMPMASSCHARGE
- Possibility to enable or disable \ref RESTART on a per action basis.
- Possibility to enable or disable \ref RESTART on a per action basis.
- \ref MOLFILE now supports many more special names for rna and dna (thanks to Alejandro Gil-Ley).
- VMEAN and VSUM allow one to calculate the sum of a set of vectors calculated by VectorMultiColvar. Note these
- VMEAN and VSUM allow one to calculate the sum of a set of vectors calculated by VectorMultiColvar. Note these
can also be used in tandem with \ref AROUND or \ref MFILTER_MORE to calculate the average vector within a particular
can also be used in tandem with \ref AROUND or \ref MFILTER_MORE to calculate the average vector within a particular
part of the cell or the average vector amonst those that have a magnitude greater than some tolerance
part of the cell or the average vector amonst those that have a magnitude greater than some tolerance
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user-doc/tutorials/moving.txt
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@@ -182,7 +182,7 @@ equivalent. You should read the documentation for the Plumed 2 Action.
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@@ -182,7 +182,7 @@ equivalent. You should read the documentation for the Plumed 2 Action.
</TR>
</TR>
<TR>
<TR>
<TD> PUCKERING </TD>
<TD> PUCKERING </TD>
<TD>
<b> currently missing </b>
</TD>
<TD>
\ref PUCKERING (5 membered rings only)
</TD>
</TR>
</TR>
<TR>
<TR>
<TD> S_PATH </TD>
<TD> S_PATH </TD>
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