Questions tagged [plumed]

Questions relating to the use of the PLUMED software.

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2 votes
1 answer

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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6 votes
1 answer

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 ...
BGK's user avatar
  • 61
3 votes
0 answers

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.
Roshan Shrestha's user avatar
7 votes
0 answers

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 ...
fireball.1's user avatar
  • 1,083