--- /ug ---


Filename: Makefile
Revision 1.74jim 2016/12/21 15:42:26+1 -1
Update to 2.12.
Show difference between Revision 1.73 and 1.74
Revision 1.73jim 2016/12/20 20:33:10+1 -1
Remove unused ug_eabf.tex file to avoid confusion.
Show difference between Revision 1.72 and 1.73
Revision 1.72jim 2016/11/01 22:01:13+1 -1
Update to 2.12b1.
Show difference between Revision 1.71 and 1.72
Revision 1.71jim 2016/10/07 21:42:39+1 -1
Add dependency.
Show difference between Revision 1.70 and 1.71
Revision 1.70jim 2016/09/27 15:40:44+1 -1
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot.
Show difference between Revision 1.69 and 1.70
Revision 1.69jim 2016/06/30 18:47:37+1 -1
Work around unusual sh echo behavior on Ubuntu when creating namd_version.tex.
Show difference between Revision 1.68 and 1.69

Filename: namd_macros.tex
Revision 1.17jim 2016/12/20 20:36:33+1 -1
Add authors Bernardi, Fu, Melo, Rudack.
Show difference between Revision 1.16 and 1.17

Filename: ug.bib
Revision 1.28jim 2017/02/06 18:54:16+5 -2
Fix "page" to "pages".
Show difference between Revision 1.27 and 1.28
Revision 1.27jim 2017/02/06 18:51:34+7 -3
Add volume and page to GaMD reference.
Show difference between Revision 1.26 and 1.27
Revision 1.26jim 2017/02/03 21:39:29+21 -2
Gaussian accelerated MD (GaMD) implementation by Andrew Pang and Yi Wang.
Show difference between Revision 1.25 and 1.26
Revision 1.25jim 2016/09/19 22:51:20+6 -3
Fix error.
Show difference between Revision 1.24 and 1.25

Filename: ug.tex
Revision 1.22jim 2016/10/07 15:54:01+2 -2
Remove separate eABF docs now included with colvars.
Show difference between Revision 1.21 and 1.22
Revision 1.21jim 2016/09/27 15:40:44+4 -1
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot.
Show difference between Revision 1.20 and 1.21

Filename: ug_accel.tex
Revision 1.18jim 2017/02/03 21:39:29+150 -0
Gaussian accelerated MD (GaMD) implementation by Andrew Pang and Yi Wang.
Show difference between Revision 1.17 and 1.18

Filename: ug_alchemy.tex
Revision 1.34jim 2016/11/07 20:28:33+59 -59
From Brian Radak, change alchBondLambdaEnd default and update thermodynamic integration documentation.
Show difference between Revision 1.33 and 1.34
Revision 1.33jim 2016/06/29 21:26:26+33 -1
From Brian Radak, alchemy doc updates.
Show difference between Revision 1.32 and 1.33

Filename: ug_colvars-cv.tex
Revision 1.3jim 2017/03/08 18:57:26+1 -0
Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041
Show difference between Revision 1.2 and 1.3
Revision 1.2jim 2017/02/08 16:58:35+7 -0
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.1 and 1.2
Revision 1.1jim 2016/10/07 16:14:18None
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 1.5jim 2017/02/08 16:58:35+2 -2
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.4 and 1.5
Revision 1.4jim 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
Show difference between Revision 1.3 and 1.4

Filename: ug_colvars.tex
Revision 1.34jim 2017/05/16 21:14:26+75 -6
Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8
Show difference between Revision 1.33 and 1.34
Revision 1.33jim 2017/03/01 14:34:08+17 -3
Update Colvars to 7c48dc02460f1f68a00c872acd964b5ff2276098
Show difference between Revision 1.32 and 1.33
Revision 1.32jim 2017/02/08 16:58:36+65 -51
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.31 and 1.32
Revision 1.31jim 2016/12/20 20:25:53+4 -3
Update eABF docs for recent changes.
Show difference between Revision 1.30 and 1.31
Revision 1.30jim 2016/11/28 17:32:06+8 -8
Colvars doc fixes from Giacomo Fiorin and Jerome Henin.
Show difference between Revision 1.29 and 1.30
Revision 1.29jim 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).
Show difference between Revision 1.28 and 1.29
Revision 1.28jim 2016/10/07 21:46:27+1 -1
Fix missing reference.
Show difference between Revision 1.27 and 1.28
Revision 1.27jim 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
Show difference between Revision 1.26 and 1.27

Filename: ug_colvars_macros.tex
Revision 1.8jim 2017/02/08 16:58:36+7 -0
Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05
Show difference between Revision 1.7 and 1.8
Revision 1.7jim 2016/11/28 17:32:06+3 -5
Colvars doc fixes from Giacomo Fiorin and Jerome Henin.
Show difference between Revision 1.6 and 1.7
Revision 1.6jim 2016/10/07 21:45:01+3 -3
Tweak index entries and fix missing references.
Show difference between Revision 1.5 and 1.6
Revision 1.5jim 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
Show difference between Revision 1.4 and 1.5

Filename: ug_eabf.bib
Revision 1.1jim 2016/09/27 15:40:44None
Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot.

Filename: ug_fenergy.tex

Filename: ug_forcefield.tex
Revision 1.23jim 2016/06/29 21:25:17+2 -2
From Brian Radak, remove LJcorrection/vdwForceSwitching warning.
Show difference between Revision 1.22 and 1.23

Filename: ug_runit.tex
Revision 1.33jim 2016/12/21 16:57:00+34 -2
Update for Omni-Path and KNL.
Show difference between Revision 1.32 and 1.33

Filename: ug_start.tex
Revision 1.33jim 2016/09/30 20:04:33+4 -0
Document move command.
Show difference between Revision 1.32 and 1.33
Revision 1.32jim 2016/09/19 22:49:40+1 -1
Fix multiply defined label.
Show difference between Revision 1.31 and 1.32
Revision 1.31jim 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".
Show difference between Revision 1.30 and 1.31


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