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Title: SSAGES: Software Suite for Advanced General Ensemble Simulations

Abstract

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods, and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this study, the use of SSAGES is illustrated in the context of simple representative applications involvingmore » distinct methods and different collective variables that are available in the current release of the suite.« less

Authors:
 [1];  [2];  [3];  [1]; ORCiD logo [4];  [4];  [4];  [4];  [4];  [4];  [4];  [4]; ORCiD logo [1]; ORCiD logo [4];  [4];  [1];  [4];  [4];  [4];  [2] more »; ORCiD logo [1];  [2] « less
  1. Univ. of Notre Dame, Notre Dame, IN (United States)
  2. Univ. of Chicago, Chicago, IL (United States); Argonne National Lab. (ANL), Lemont, IL (United States)
  3. Univ. of Chicago, Chicago, IL (United States); Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen (Germany)
  4. Univ. of Chicago, Chicago, IL (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Materials Sciences & Engineering Division; Midwest Integrated Center for Computational Materials (MICCoM); National Science Foundation (NSF); USDOE
OSTI Identifier:
1422554
Alternate Identifier(s):
OSTI ID: 1417717
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 148; Journal Issue: 4; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING

Citation Formats

Sidky, Hythem, Colon, Yamil J., Helfferich, Julian, Sikora, Benjamin J., Bezik, Cody, Chu, Weiwei, Giberti, Federico, Guo, Ashley Z., Jiang, Xikai, Lequieu, Joshua, Li, Jiyuan, Moller, Joshua, Quevillon, Michael J., Rahimi, Mohammad, Ramezani-Dakhel, Hadi, Rathee, Vikramjit S., Reid, Daniel R., Sevgen, Emre, Thapar, Vikram, Webb, Michael A., Whitmer, Jonathan K., and de Pablo, Juan J.. SSAGES: Software Suite for Advanced General Ensemble Simulations. United States: N. p., 2018. Web. doi:10.1063/1.5008853.
Sidky, Hythem, Colon, Yamil J., Helfferich, Julian, Sikora, Benjamin J., Bezik, Cody, Chu, Weiwei, Giberti, Federico, Guo, Ashley Z., Jiang, Xikai, Lequieu, Joshua, Li, Jiyuan, Moller, Joshua, Quevillon, Michael J., Rahimi, Mohammad, Ramezani-Dakhel, Hadi, Rathee, Vikramjit S., Reid, Daniel R., Sevgen, Emre, Thapar, Vikram, Webb, Michael A., Whitmer, Jonathan K., & de Pablo, Juan J.. SSAGES: Software Suite for Advanced General Ensemble Simulations. United States. doi:10.1063/1.5008853.
Sidky, Hythem, Colon, Yamil J., Helfferich, Julian, Sikora, Benjamin J., Bezik, Cody, Chu, Weiwei, Giberti, Federico, Guo, Ashley Z., Jiang, Xikai, Lequieu, Joshua, Li, Jiyuan, Moller, Joshua, Quevillon, Michael J., Rahimi, Mohammad, Ramezani-Dakhel, Hadi, Rathee, Vikramjit S., Reid, Daniel R., Sevgen, Emre, Thapar, Vikram, Webb, Michael A., Whitmer, Jonathan K., and de Pablo, Juan J.. Mon . "SSAGES: Software Suite for Advanced General Ensemble Simulations". United States. doi:10.1063/1.5008853. https://www.osti.gov/servlets/purl/1422554.
@article{osti_1422554,
title = {SSAGES: Software Suite for Advanced General Ensemble Simulations},
author = {Sidky, Hythem and Colon, Yamil J. and Helfferich, Julian and Sikora, Benjamin J. and Bezik, Cody and Chu, Weiwei and Giberti, Federico and Guo, Ashley Z. and Jiang, Xikai and Lequieu, Joshua and Li, Jiyuan and Moller, Joshua and Quevillon, Michael J. and Rahimi, Mohammad and Ramezani-Dakhel, Hadi and Rathee, Vikramjit S. and Reid, Daniel R. and Sevgen, Emre and Thapar, Vikram and Webb, Michael A. and Whitmer, Jonathan K. and de Pablo, Juan J.},
abstractNote = {Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods, and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this study, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite.},
doi = {10.1063/1.5008853},
journal = {Journal of Chemical Physics},
number = 4,
volume = 148,
place = {United States},
year = {Mon Jan 22 00:00:00 EST 2018},
month = {Mon Jan 22 00:00:00 EST 2018}
}

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