Filename: Makefile | |||
Revision 1.74 | jim | 2016/12/21 15:42:26 | +1 -1 |
Update to 2.12. | |||
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Revision 1.73 | jim | 2016/12/20 20:33:10 | +1 -1 |
Remove unused ug_eabf.tex file to avoid confusion. | |||
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Revision 1.72 | jim | 2016/11/01 22:01:13 | +1 -1 |
Update to 2.12b1. | |||
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Revision 1.71 | jim | 2016/10/07 21:42:39 | +1 -1 |
Add dependency. | |||
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Revision 1.70 | jim | 2016/09/27 15:40:44 | +1 -1 |
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. | |||
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Revision 1.69 | jim | 2016/06/30 18:47:37 | +1 -1 |
Work around unusual sh echo behavior on Ubuntu when creating namd_version.tex. | |||
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Filename: namd_macros.tex | |||
Revision 1.17 | jim | 2016/12/20 20:36:33 | +1 -1 |
Add authors Bernardi, Fu, Melo, Rudack. | |||
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Filename: ug.bib | |||
Revision 1.28 | jim | 2017/02/06 18:54:16 | +5 -2 |
Fix "page" to "pages". | |||
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Revision 1.27 | jim | 2017/02/06 18:51:34 | +7 -3 |
Add volume and page to GaMD reference. | |||
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Revision 1.26 | jim | 2017/02/03 21:39:29 | +21 -2 |
Gaussian accelerated MD (GaMD) implementation by Andrew Pang and Yi Wang. | |||
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Revision 1.25 | jim | 2016/09/19 22:51:20 | +6 -3 |
Fix error. | |||
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Filename: ug.tex | |||
Revision 1.22 | jim | 2016/10/07 15:54:01 | +2 -2 |
Remove separate eABF docs now included with colvars. | |||
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Revision 1.21 | jim | 2016/09/27 15:40:44 | +4 -1 |
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. | |||
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Filename: ug_accel.tex | |||
Revision 1.18 | jim | 2017/02/03 21:39:29 | +150 -0 |
Gaussian accelerated MD (GaMD) implementation by Andrew Pang and Yi Wang. | |||
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Filename: ug_alchemy.tex | |||
Revision 1.34 | jim | 2016/11/07 20:28:33 | +59 -59 |
From Brian Radak, change alchBondLambdaEnd default and update thermodynamic integration documentation. | |||
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Revision 1.33 | jim | 2016/06/29 21:26:26 | +33 -1 |
From Brian Radak, alchemy doc updates. | |||
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Filename: ug_colvars-cv.tex | |||
Revision 1.3 | jim | 2017/03/08 18:57:26 | +1 -0 |
Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041 | |||
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Revision 1.2 | jim | 2017/02/08 16:58:35 | +7 -0 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
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Revision 1.1 | jim | 2016/10/07 16:14:18 | None |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts |
Filename: ug_colvars.bib | |||
Revision 1.5 | jim | 2017/02/08 16:58:35 | +2 -2 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
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Revision 1.4 | jim | 2016/10/07 16:14:18 | +69 -0 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
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Filename: ug_colvars.tex | |||
Revision 1.34 | jim | 2017/05/16 21:14:26 | +75 -6 |
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 | |||
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Revision 1.33 | jim | 2017/03/01 14:34:08 | +17 -3 |
Update Colvars to 7c48dc02460f1f68a00c872acd964b5ff2276098 | |||
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Revision 1.32 | jim | 2017/02/08 16:58:36 | +65 -51 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
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Revision 1.31 | jim | 2016/12/20 20:25:53 | +4 -3 |
Update eABF docs for recent changes. | |||
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Revision 1.30 | jim | 2016/11/28 17:32:06 | +8 -8 |
Colvars doc fixes from Giacomo Fiorin and Jerome Henin. | |||
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Revision 1.29 | jim | 2016/10/24 21:16:00 | +10 -1 |
From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). | |||
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Revision 1.28 | jim | 2016/10/07 21:46:27 | +1 -1 |
Fix missing reference. | |||
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Revision 1.27 | jim | 2016/10/07 16:14:18 | +1060 -309 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
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Filename: ug_colvars_macros.tex | |||
Revision 1.8 | jim | 2017/02/08 16:58:36 | +7 -0 |
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 | |||
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Revision 1.7 | jim | 2016/11/28 17:32:06 | +3 -5 |
Colvars doc fixes from Giacomo Fiorin and Jerome Henin. | |||
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Revision 1.6 | jim | 2016/10/07 21:45:01 | +3 -3 |
Tweak index entries and fix missing references. | |||
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Revision 1.5 | jim | 2016/10/07 16:14:18 | +10 -41 |
Colvars update from Giacomo Fiorin and Jerome Henin. - Parallel calculation of center-of-mass based variables - Shared-memory parallel calculation of many variables (requires CkLoop) - Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md - Extended-system ABF method by the CZAR estimator - Histogram calculation on ensembles of variables, with optional weights - Probability distribution restraints - Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield) - Scripting command "cvcflags" to optimize performance of complex colvars - Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods - Improved error handling in user input and Tcl scripts | |||
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Filename: ug_eabf.bib | |||
Revision 1.1 | jim | 2016/09/27 15:40:44 | None |
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
Filename: ug_fenergy.tex | |||
Filename: ug_forcefield.tex | |||
Revision 1.23 | jim | 2016/06/29 21:25:17 | +2 -2 |
From Brian Radak, remove LJcorrection/vdwForceSwitching warning. | |||
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Filename: ug_runit.tex | |||
Revision 1.33 | jim | 2016/12/21 16:57:00 | +34 -2 |
Update for Omni-Path and KNL. | |||
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Filename: ug_start.tex | |||
Revision 1.33 | jim | 2016/09/30 20:04:33 | +4 -0 |
Document move command. | |||
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Revision 1.32 | jim | 2016/09/19 22:49:40 | +1 -1 |
Fix multiply defined label. | |||
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Revision 1.31 | jim | 2016/09/18 22:24:39 | +12 -0 |
Add --tclmain and +tclsh options to allow passing of command-line arguments to a Tcl script either with (--tclmain) or without (+tclsh) Charm++ startup and NAMD scripting features. E.g., "./namd2 +tclsh script.tcl arg1 arg2". | |||
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