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Martin Kurečka
Plumed AlphaFold
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42f78b2f
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Commit
42f78b2f
authored
10 years ago
by
Carlo Camilloni
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belfast-8: typos
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user-doc/tutorials/belfast-8.txt
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user-doc/tutorials/belfast-8.txt
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42f78b2f
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@@ -8,7 +8,7 @@ the input files for BEMETA for a simple case of three alanines and we will use M
the results of WT-BEMETA and STANDARD-BEMETA with four independent runs on the four Collective Variables. Finally we will
use a simplified version of BEMETA that is Multiple Walkers Metadynamics.
\section belfast-
1
-lo Learning Outcomes
\section belfast-
8
-lo Learning Outcomes
Once this tutorial is completed students will:
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@@ -65,7 +65,7 @@ In the following example, a bias-exchange simulation is performed on a Val-Ile-L
Four replicas of the system are employed, each one biased on a different CV,
thus four similar Plumed input files are prepared as follows:
- a common input file in which all the collective variables are define:
- a common input file in which all the collective variables are define
d
:
\verbatim
MOLINFO STRUCTURE=VIL.pdb
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@@ -78,9 +78,9 @@ cv4: TORSION ATOMS=@phi-3
\endverbatim
NOTE:
1. By using \ref MOLINFO we can use shortcut to select atoms for dihedral angles (currently @phi, @psi, @omega and @chi1 are
1. By using \ref MOLINFO we can use shortcut to select atoms for dihedral angles (currently
\
@phi,
\
@psi,
\
@omega and
\
@chi1 are
available).
2. We use cv# as label in order to make the output compatible with METAGUI.
2. We use cv# as label
s
in order to make the output compatible with METAGUI.
3. \ref RANDOM_EXCHANGES generates random exchanges list that are sent back to GROMACS.
- four additional input files that \ref INCLUDE the common input and define the four \ref METAD along the four CVs, respectively.
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@@ -95,7 +95,6 @@ NOTE:
1. in COLVAR we \ref PRINT only the four collective variables, always in the same order in such a way that COLVARs are compatible
with METAGUI
2. if you want to print additional information, like the \ref METAD bias it is possibile to use additional \ref PRINT keyword
3. Originally Bias-Exchange has been used without Well-Tempered Metadynamics but nothing prevents its use.
\verbatim
PRINT ARG=cv1,be.bias STRIDE=xxx FILE=BIAS
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