Surjit B. Dixit, Jerome Henin, Christophe Chipot  Home/Search
Context
Related
| uiuc.edu/Research/n...AlchemicalFEP.pdf Cached: PS.gz PS PDF This document uses CoBlitz to cache paper downloads. If your firewall is blocking outgoing connections to port 3125, you can use these links to download local copies.
Image Update HelpPS.gz PS PDF From: uiuc.edu/Research/namd/namd (more) (Enter author homepages) |
Rate this article:      (best)Comment on this article |
Abstract: Introduction The main goal of this tutorial is to provide a guidance when setting up free energy calculations of alchemical transformations within NAMD. As has been commented on amply, such in silico experiments have not reached yet the maturity to be viewed as black--box, routine jobs. Either the set--up, the sampling protocol, or the analysis of the result should be considered with great care. The paradigm chosen in NAMD for performing alchemical transformations is the so--called... (Update)
Active bibliography (related documents): More All
1.2: NAMD User's Guide - Version 2.5 - Bhandarkar, Brunner, Chipot, Dalke.. (2003) (Correct)
0.5: Special Purpose Parallel Computing - McColl (1993) (Correct)
0.5: Contributions to the Binding Free Energy of Ligands to .. - Lazaridis, Masunov.. (2002) (Correct)
Similar documents based on text: More All
0.6: Scalable Molecular Dynamics for Large Biomolecular Systems - Brunner, Phillips.. (2000) (Correct)
0.1: Markov Extensions For Multi-Dimensional Dynamical Systems - Buzzi (1999) (Correct)
0.1: Automatic Motion Planning for Complex Articulated Bodies - Barraquand (1991) (Correct)
BibTeX entry: (Update)
@misc{ dixit-tutorial,
author = "Surjit B. Dixit and Jerome Henin and Christophe Chipot",
title = "A Tutorial to Set up Alchemical Free Energy Perturbation Calculations in
NAMD",
url = "citeseer.ist.psu.edu/dixit04tutorial.html" }
Citations (may not include all citations):120 CHARMM: A program for macromolecular energy (context) - Brooks, Bruccoleri et al. - 1983
5 Free energy calculations: Applications to chemical and bioch.. (context) - Kollman - 1993
2 Can absolute free energies of association be estimated from .. (context) - Dixit, Chipot - 2001
2 the long and winding gilded road (context) - Chipot, Pearlman et al. - 2002
2 A comparison of alternative approaches to free energy calcul.. (context) - Pearlman - 1994
2 Free energy calculations by computer simulation (context) - Bash, Singh et al. - 1987
1 Free energy via molecular simulation: A primer (context) - Beveridge, DiCapua - 1989
1 A comparison of non--bonded scaling approaches for free ener.. (context) - Pitera, van Gunsteren - 2002
1 Affinities of amino acid side chains for solvent water (context) - Wolfenden, Andersson et al. - 1981
1 Free energy perturbation calculations: Problems and pitfalls.. (context) - Pearlman, Kollman - 1989
1 The overlooked bond--stretching contribution in free energy .. (context) - Pearlman, Kollman - 1991
Documents on the same site (http://www.ks.uiuc.edu/Research/namd/namd.html): More
NAMD User's Guide - Bhandarkar, Brunner, Dalke.. (2000) (Correct)
NAMD User's Guide - Version 2.2 - Bhandarkar, Brunner, Dalke.. (2000) (Correct)
NAMD User's Guide - Version 2.5 - Bhandarkar, Brunner, Chipot, Dalke.. (2003) (Correct)
Online articles have much greater impact More about CiteSeer.IST Add search form to your site Submit documents Feedback
CiteSeer.IST - Copyright Penn State and NEC