Questions tagged [plumed]
Questions relating to the use of the PLUMED software.
4
questions
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votes
1
answer
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Adding new CVs to a Storage
I am trying to add a new CV (A plumed one) to a storage. I've completed a TPS simulation, and now I want to store the new CV for later analysis use.
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user7624
6
votes
1
answer
77
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What is the largest number of collective variables used in a metadynamics simulation?
Metadynamics is usually used to construct 1D or 2D free-energy surfaces. There seem to be a few examples for 3D free-energy surfaces:
Paper 1: Exploring the Free Energy Landscape of Solutes Embedded ...
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3
votes
0
answers
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Stress on pulling in MD simulation [closed]
In gromacs, if we use SMD to pull one end of the molecule, how can we compute the stress applied if we know the force. I am using plumed to define a colvar, and pulling one end of my molecule. Thanks.
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7
votes
0
answers
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Collective variable to determine the number of bonds in the shortest Hydrogen bond wire [closed]
I am trying to program a collective variable in PLUMED which is basically the number of bonds in the shortest Hydrogen bond wire in a system of water molecules. I plan to use the HBond_Matrix from ...
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