Questions tagged [enhanced-sampling]
Questions about or related to enhanced sampling.
7 questions
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How the center of mass of a large number of atoms influences the performance of Amber in a system?
I'm interested in conducting umbrella sampling between a ligand and the center of mass of a lipid. Initially, I chose the atom numbers for the ligand and all the atom numbers for the lipids. However, ...
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How can I specify the direction of motion in the colvars file?
I am doing umbrella sampling in NAMD and I want to control the distance in the colvars to be in one direction. Is there any possibility?
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How can a harmonic constraint be added between two groups in one direction using NAMD?
As a new user of NAMD, I am seeking assistance regarding a specific task. I intend to pull a LIGAND from outside to the center of a lipid using NAMD. To achieve this, I have utilized the colvar module ...
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How to perform a rotation of a structure, specifically throughout molecular dynamics or umbrella sampling simulations?
I have a structure, as depicted in the figure, which is a part of a longer chain. The portion within the red circle is predominantly parallel. My objective is to rotate this part, aiming to orient the ...
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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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Is it required to sample the full reaction coordinate in umbrella sampling?
Below is the free energy profile obtained after a histogram analysis of an umbrella sampling simulation. Generally, one is interested in the free energy difference (highest energy minus lowest energy)....
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How to choose replica exchange interval?
I was wondering what goes into the consideration of choosing the frequency to attempt swaps for replica exchange? D. Sindhikara, 2008 proposes the faster the better, but this goes against the view ...
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