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Martin Kurečka
Plumed AlphaFold
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ffe6aca0
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ffe6aca0
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11 years ago
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Giovanni Bussi
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Added note on BIASFACTOR and RESTART
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@@ -88,6 +88,9 @@ V({s},t)= \sum_{t'=0,\tau_G,2\tau_G,\dots}^{t'<t} W e^{-V({s}({q}(t'),t')/\Delta
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@@ -88,6 +88,9 @@ V({s},t)= \sum_{t'=0,\tau_G,2\tau_G,\dots}^{t'<t} W e^{-V({s}({q}(t'),t')/\Delta
This method ensures that the bias converges more smoothly. It should be noted that, in the case of well-tempered metadynamics, in
This method ensures that the bias converges more smoothly. It should be noted that, in the case of well-tempered metadynamics, in
the output printed the Gaussian height is re-scaled using the bias factor.
the output printed the Gaussian height is re-scaled using the bias factor.
Also notice that with well-tempered metadynamics the HILLS file does not contain the bias,
but the negative of the free-energy estimate. This choice has the advantage that
one can restart a simulation using a different value for the \f$\Delta T\f$. The applied bias will be scaled accordingly.
Note that you can use here also the flexible gaussian approach \cite Branduardi:2012dl
Note that you can use here also the flexible gaussian approach \cite Branduardi:2012dl
in which you can adapt the gaussian to the extent of Cartesian space covered by a variable or
in which you can adapt the gaussian to the extent of Cartesian space covered by a variable or
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