TY - JOUR
T1 - On-the-fly string method for minimum free energy paths calculation
AU - Maragliano, Luca
AU - Vanden-Eijnden, Eric
N1 - Funding Information:
The ideas presented here were discussed during a meeting organized at CECAM in February 2007 with Giovanni Ciccotti, Mauro Ferrario, Maddalena Venturoli and Rodolphe Vuilleumier. We thank them all for their useful suggestions, and we are grateful to Berend Smit for making the meeting possible. We also want to warmly thank Ron Elber for useful discussions and help with MOIL code, Giovanni Ciccotti for his careful reading of the manuscript and Weinan E. for discussions about concurrent coupling. L.M. is grateful to COST for partial support under its Action P13. This work was partially supported by NSF Grants DMS02-09959 and DMS02-39625, and by ONR Grant N00014-04-1-0565.
PY - 2007/9/26
Y1 - 2007/9/26
N2 - An improved and simplified version of the string method in collective variables for computing minimum free energy paths is proposed. The string is discretized into a finite number of images and in the new method these images are evolved concurrently with replicas of the original system while keeping their inter-distances equal via reparametrization. There is no need to compute the mean force by time-averaging, nor to project the force perpendicularly to the string. In this Letter, the algorithmic aspects of the on-the-fly string method are presented in detail and the method is tested on the solvated alanine dipeptide molecule.
AB - An improved and simplified version of the string method in collective variables for computing minimum free energy paths is proposed. The string is discretized into a finite number of images and in the new method these images are evolved concurrently with replicas of the original system while keeping their inter-distances equal via reparametrization. There is no need to compute the mean force by time-averaging, nor to project the force perpendicularly to the string. In this Letter, the algorithmic aspects of the on-the-fly string method are presented in detail and the method is tested on the solvated alanine dipeptide molecule.
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U2 - 10.1016/j.cplett.2007.08.017
DO - 10.1016/j.cplett.2007.08.017
M3 - Article
AN - SCOPUS:34548535576
VL - 446
SP - 182
EP - 190
JO - Chemical Physics Letters
JF - Chemical Physics Letters
SN - 0009-2614
IS - 1-3
ER -