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• 13:29, 20 June 2026 Kulhanek talk contribs created page STM:Collective Variables (Created page with "Navigation: Documentation / Methods / String Method / STM:Client / STM:Collective Variables ---- __NOEDITSECTION__ __NOTOC__ Each collective variable used in a string method simulation is specified in a separate [CV] section. These sections are placed either in a special group, {STM} by default, when the collective variables are defined in the main control file, or in the {MAIN} group of a separate file. The name of the group or the file is controlled...")
• 13:21, 20 June 2026 Kulhanek talk contribs created page ABP:Collective Variables (Created page with "Navigation: Documentation / Methods / Constrained Dynamics / CST:Constraints __NOEDITSECTION__ __NOTOC__ ---- Each collective variable employed by the Adaptive Biasing Potential (ABP) method is provided in a separate [CV] section. These sections are placed either in a special group, {ABP} by default, when the collective variables are defined in the main control file, or in the {MAIN} group of a separate file. The name of the group or the file is controlle...")
• 07:52, 20 June 2026 Kulhanek talk contribs created page ABP:Files (Created page with "Navigation: Documentation / Methods / Constrained Dynamics / ABP:Files ----")
• 07:52, 20 June 2026 Kulhanek talk contribs created page ABP:Examples (Created page with "Navigation: Documentation / Methods / Constrained Dynamics / ABP:Examples ----")
• 07:39, 20 June 2026 Kulhanek talk contribs created page ABP:Controls (Created page with "## Navigation: Documentation / Methods / Adaptive Biasing Potential / ABP:Controls **NOEDITSECTION** **NOTOC** The behaviour of the Adaptive Biasing Potential (ABP) method is controlled by the setup provided in the [abp] section. This section belongs to the {PMFLIB} group. The ABP method implemented in PMFLib calculates the mollified free energy from a smoothed population of selected collective variables. The obtained free-energy surface is therefore no...")
• 07:30, 20 June 2026 Kulhanek talk contribs created page ABP:Utilities (Created page with "Navigation: Documentation / Methods / Constrained Dynamics / ABP:Utilities __NOEDITSECTION__ ---- The CST data can be processed by the following utilities. * CST accumulator processing (only if <i>freadranges</i> is <i>on</i>). ** accu-info ** accu-combine ** accu-trajectory * The free energy, internal energy, entropic contribution and other data: ** pmf-integrate")
• 07:01, 20 June 2026 Kulhanek talk contribs created page CST:Files (Created page with "Navigation: Documentation / Methods / Constrained Dynamics / CST:Files ----")
• 13:50, 19 June 2026 Kulhanek talk contribs created page MON:Examples (Created page with "Navigation: Documentation / Methods / Collective Variable Monitoring / MON:Examples ----")
• 13:50, 19 June 2026 Kulhanek talk contribs created page PDRV:Examples (Created page with "Navigation: Documentation / Methods / Path Driving / PDRV:Examples ----")
• 12:11, 19 June 2026 Kulhanek talk contribs created page Metric Tensor Analysis (Created page with "Navigation: Documentation / Methods / Metric Tensor Analysis")
• 11:54, 19 June 2026 Kulhanek talk contribs created page Template:CSTUtils (Created page with "__NOTOC__ <div style="float:right; border-style: solid; border-width: 1px; border-color: #aaaaaa; background-color: #f6f6f6; padding: 0px; width: 10em;"> <h1 style="margin:2px 2px 0px 2px; border: none; background-color: #87cefa; text-align: center; font-size: 1.0em; color: blue; padding: 2px;">CST Utilities</h1> <div style="margin: 5px; font-size: 0.8em;"> * pmf-integrate </div> </div>")
• 11:50, 19 June 2026 Maintenance script talk contribs created page Pmf-energy
• 11:50, 19 June 2026 Maintenance script talk contribs created page Aus-integrate
• 21:54, 2 June 2026 Kulhanek talk contribs created page STM:Path (Created page with "Navigation: Documentation / Methods / String Method / STM:Client / STM:Path ---- __NOEDITSECTION__ __NOTOC__")
• 21:09, 2 June 2026 Kulhanek talk contribs created page STM:Server Controls (Created page with "Navigation: Documentation / Methods / String Method / STM:Server / STM:Server Controls ---- __NOEDITSECTION__ __NOTOC__")
• 21:09, 2 June 2026 Kulhanek talk contribs created page STM::Server Controls (Created page with "Navigation: Documentation / Methods / String Method / STM:Server / STM:Server Controls ---- __NOEDITSECTION__ __NOTOC__")
• 21:08, 2 June 2026 Kulhanek talk contribs created page STM:Server (Created page with "Navigation: Documentation / Methods / String Method / STM:Client ---- __NOEDITSECTION__ __NOTOC__")
• 20:40, 2 June 2026 Kulhanek talk contribs created page Metric Tensor Correction (Created page with "Navigation: Documentation / Methods / Metric Tensor Correction")
• 18:51, 2 June 2026 Kulhanek talk contribs created page STM:Client Controls (Created page with "Navigation: Documentation / Methods / String Method / STM:Client / STM:Client Controls ---- __NOEDITSECTION__ __NOTOC__ The behavior of the string method is configured in the [stm] section, which is part of the {PMFLIB} group. ==[stm]== {| style="width: 100%;" | style="width: 10em;" | '''Key''' | style="width: 10em;" | '''Default value''' | style="width: 5em;" | '''Type''' | '''Description''' |- style="vertical-align: top; background-color: #f6f6f6;...")
• 18:49, 2 June 2026 Kulhanek talk contribs created page STM:Client (Created page with "Navigation: Documentation / Methods / String Method / STM:Client ---- __NOEDITSECTION__ __NOTOC__")
• 17:59, 2 June 2026 Kulhanek talk contribs created page File:MTC-STM-d1d2-01.apng
• 17:59, 2 June 2026 Kulhanek talk contribs uploaded File:MTC-STM-d1d2-01.apng
• 15:02, 2 June 2026 Kulhanek talk contribs uploaded a new version of File:Movie.png
• 14:58, 2 June 2026 Kulhanek talk contribs uploaded a new version of File:Movie.png
• 14:52, 2 June 2026 Kulhanek talk contribs created page File:Movie.png
• 14:52, 2 June 2026 Kulhanek talk contribs uploaded File:Movie.png
• 19:59, 28 May 2026 Kulhanek talk contribs created page CV:PTPATHZ (Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:PTPATHZ ---- {{CVS}} ===Definition=== The soft minimum squared distance between the center of mass of the anchor group and a set of explicitly defined reference points. Each reference point is represented by the center of mass of one atom group. For the anchor center of mass <math>\boldsymbol A_{com}</math> and the centers of mass of the reference points <math>\boldsymbol R_{i,com}</math...")
• 19:55, 28 May 2026 Kulhanek talk contribs created page CV:PTPATHS2PN (Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:PTPATHS2PN ---- {{CVS}} ===Definition=== The signed path coordinate of the center of mass of the anchor group along a linear path defined by a reference point and a direction. The reference point and the direction point are represented by the centers of mass of two atom groups. Let <math>\boldsymbol A_{com}</math> be the anchor center of mass, <math>\boldsymbol R_{com}</math> the center...")
• 19:53, 28 May 2026 Kulhanek talk contribs created page CV:PTPATHS2P (Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:PTPATHS2P ---- {{CVS}} ===Definition=== The path coordinate of the center of mass of the anchor group along a linear path generated from two reference points. The two reference points are represented by the centers of mass of two atom groups. Let <math>\boldsymbol A_{com}</math> be the anchor center of mass and <math>\boldsymbol R_{1,com}</math> and <math>\boldsymbol R_{2,com}</math> be...")
• 19:48, 28 May 2026 Kulhanek talk contribs created page CV:PTPATHS (Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:PTPATHS ---- {{CVS}} ===Definition=== The path coordinate of the center of mass of the anchor group relative to a set of explicitly defined reference points. Each reference point is represented by the center of mass of one atom group. For the anchor center of mass <math>\boldsymbol A_{com}</math> and the centers of mass of the reference points <math>\boldsymbol R_{i,com}</math>, the coll...")
• 19:46, 28 May 2026 Kulhanek talk contribs created page PTPATHS (Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:PTPATHS ---- {{CVS}} ===Definition=== The path coordinate of the center of mass of the anchor group relative to a set of explicitly defined reference points. Each reference point is represented by the center of mass of one atom group. For the anchor center of mass <math>\boldsymbol A_{com}</math> and the centers of mass of the reference points <math>\boldsymbol R_{i,com}</math>, the coll...")
• 12:33, 21 June 2021 Kulhanek talk contribs uploaded File:Worm.png
• 11:47, 21 June 2021 Kulhanek talk contribs uploaded File:Bpp.png
• 11:43, 21 June 2021 Kulhanek talk contribs uploaded File:Stp.png
• 17:08, 12 February 2019 Kulhanek talk contribs uploaded File:Puckering.png
• 17:08, 12 February 2019 Kulhanek talk contribs deleted page File:Puckering.png
• 15:12, 12 February 2019 Kulhanek talk contribs uploaded File:SF3.png (Simple Base Pair Parameters)
• 08:18, 3 July 2018 Kulhanek talk contribs changed group membership for Sysop: granted administrator and bureaucrat
• 08:17, 3 July 2018 User account Sysop talk contribs was created by Kulhanek talk contribs
• 09:04, 15 June 2015 Tbouchal talk contribs uploaded a new version of File:Puckering.png
• 08:52, 15 June 2015 Tbouchal talk contribs uploaded File:Puckering.png