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Protocols

Colvars specifications

Information


Unique identifier OMICS_28419
Name Colvars
Alternative name Collective Variables Module
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Giacomo Fiorin

Publication for Collective Variables Module

Colvars citations

 (9)
library_books

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

2018
PMCID: 5920944
PMID: 29297679
DOI: 10.1021/acs.chemrev.7b00427

[…] ee ).Easy-to-detect unstable behavior of metadynamics when the chosen CVs are not sufficient is perhaps one reason why the community using this method has developed a large number of CVs. PLUMED, and colvars are software plugins that implement a very large number of possible CVs and can be used both with metadynamics and with other CV-based enhanced sampling methods. Having a large database of imp […]

call_split

Iodide Binding in Sodium Coupled Cotransporters

2017
J Chem Inf Model
PMCID: 5744185
PMID: 29131623
DOI: 10.1021/acs.jcim.7b00521
call_split See protocol

[…] i.e. the transition coordinate for the segment beginning at point i was si = (R – pi)·(pi+1 – pi)/|pi+1 – pi|, where R is the position of the iodide ion. The ABF calculations were performed using the Colvars module of NAMD v2.10. The domain of each calculation was 0 ≤ si ≤ 3.5 Å, and force samples were collected in bins having widths of 0.1 Å to capture small-scale variations in the PMF. All calcu […]

call_split

Simple MD based model for oxidative folding of peptides and proteins

2017
Sci Rep
PMCID: 5570944
PMID: 28839177
DOI: 10.1038/s41598-017-09229-7
call_split See protocol

[…] CUDA version of pmemd to record MD data; it also calls upon other python scripts, e.g. to analyze sulfur-sulfur distances. We note that in principle the well-established interfaces such as PLUMED or COLVARS can be adapted to service the protocol described in this paper.The simulations were conducted using in-house GPU workstations in the Laboratory of Biomolecular NMR at SPbU. The production rate […]

library_books

Single molecule FRET unveils induced fit mechanism for substrate selectivity in flap endonuclease 1

2017
eLife
PMCID: 5358979
PMID: 28230529
DOI: 10.7554/eLife.21884.021

[…] scripts in VMD ().The effective free-energy profile (potential of mean force; PMF) for bending the NonEQ DF-6,1 DNA substrate was estimated using the adaptive biasing force (ABF) method (; ) with the COLVARS module of NAMD 2.11 (). ABF is a widely used enhanced sampling approach, which computes average forces along a predefined reaction coordinate (RC) and then applies an adaptive biasing potentia […]

call_split

Aminoglycoside binding and catalysis specificity of aminoglycoside 2″ phosphotransferase IVa: A thermodynamic, structural and kinetic study

2016
Biochim Biophys Acta
PMCID: 4769084
PMID: 26802312
DOI: 10.1016/j.bbagen.2016.01.016
call_split See protocol

[…] the aminoglycoside from the APH binding site, a reaction coordinate was defined as the distance separating the center of mass of each entity (antibiotic and protein). A biased force was applied using Colvars module of NAMD in order to estimate the free energy change along the reaction coordinates using the ABF method . The distance separating the two centers of mass was initially 7.5 Å and forced […]

call_split

Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non interacting Molecular Fragments

2015
PLoS Comput Biol
PMCID: 4624691
PMID: 26505197
DOI: 10.1371/journal.pcbi.1004368
call_split See protocol

[…] periments were properly normalized, namely, ∑{bin n}h¯ij(n)Δr=∑{bin n}Hij(n)Δr=1 for all the ij pair of spin-labels. The energy restraint has been introduced into NAMD under the collective variables (colvars) module. The force constant K was set to 500 kcal/mol/Å2, and the natural spread σ of the Gaussian was set to 1.1 Å. The bin width Δr was set to 1 Å and n = 1, …, 60. The backbone of the T4L w […]


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Colvars institution(s)
Department of Chemistry and Institute for Computational Molecular Science, Temple University, Philadelphia, PA, USA; Laboratoire de Biochimie Theorique, Institut de Biologie Physico-Chimique, CNRS, Paris, France
Colvars funding source(s)
Supported by NSF grant CHE1212416.

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