Molecular Dynamics

Molecular Dynamics

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A List of Solutions to Some WARNINGs in CHARMM Simulation Package

There are many types of warnings that appear in CHARMM. Here are the possible solutions for some of them. 1. "Element negative. No operation" from the SCALAR module e.g. CHARMM> scalar sca4 sum sca5 ! + <y^2> CHARMM> scalar sca4...

Published 05-17-2010 1:40 PM by StevenWang

Filed under: CHARMM
Secondary Structure Bias in Generalized Born Solvent Models

Normal 0 false false false EN-US ZH-CN X-NONE Secondary Structure Bias in Generalized Born Solvent Models: Comparison of Conformational Ensembles and Free Energy of Solvent Polarization from Explicit and Implicit Solvation Daniel R. Roe, Asim Okur, Lauren...

Published 03-13-2010 8:04 AM by cshi
Monte-carlo sampling of alchemical degrees of freedom

Molecular dynamics is routinely used to calculate free-energy changes associated with alchemical transformations. The free-energy differences can be used for many practical purposes such as drug screening, pKa calculations, and determining solvation energies...

Published 02-21-2010 11:21 AM by Jason

Filed under: free-energy, alchemical transformation, monte-carlo