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20 June 2026

• 13:2913:29, 20 June 2026 STM:Collective Variables (hist | edit) [1,327 bytes] Kulhanek (talk | contribs) (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...")
• 13:2113:21, 20 June 2026 ABP:Collective Variables (hist | edit) [2,452 bytes] Kulhanek (talk | contribs) (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...")
• 07:5207:52, 20 June 2026 ABP:Files (hist | edit) [1,148 bytes] Kulhanek (talk | contribs) (Created page with "Navigation: Documentation / Methods / Constrained Dynamics / ABP:Files ----")
• 07:5207:52, 20 June 2026 ABP:Examples (hist | edit) [107 bytes] Kulhanek (talk | contribs) (Created page with "Navigation: Documentation / Methods / Constrained Dynamics / ABP:Examples ----")
• 07:3907:39, 20 June 2026 ABP:Controls (hist | edit) [4,425 bytes] Kulhanek (talk | contribs) (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...")
• 07:3007:30, 20 June 2026 ABP:Utilities (hist | edit) [375 bytes] Kulhanek (talk | contribs) (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")
• 07:0107:01, 20 June 2026 CST:Files (hist | edit) [91 bytes] Kulhanek (talk | contribs) (Created page with "Navigation: Documentation / Methods / Constrained Dynamics / CST:Files ----")

19 June 2026

• 13:5013:50, 19 June 2026 MON:Examples (hist | edit) [104 bytes] Kulhanek (talk | contribs) (Created page with "Navigation: Documentation / Methods / Collective Variable Monitoring / MON:Examples ----")
• 13:5013:50, 19 June 2026 PDRV:Examples (hist | edit) [87 bytes] Kulhanek (talk | contribs) (Created page with "Navigation: Documentation / Methods / Path Driving / PDRV:Examples ----")
• 12:1112:11, 19 June 2026 Metric Tensor Analysis (hist | edit) [72 bytes] Kulhanek (talk | contribs) (Created page with "Navigation: Documentation / Methods / Metric Tensor Analysis")
• 11:5011:50, 19 June 2026 Pmf-energy (hist | edit) [8,902 bytes] Maintenance script (talk | contribs)
• 11:5011:50, 19 June 2026 Aus-integrate (hist | edit) [10,231 bytes] Maintenance script (talk | contribs)

2 June 2026

• 21:5421:54, 2 June 2026 STM:Path (hist | edit) [128 bytes] Kulhanek (talk | contribs) (Created page with "Navigation: Documentation / Methods / String Method / STM:Client / STM:Path ---- __NOEDITSECTION__ __NOTOC__")
• 21:0921:09, 2 June 2026 STM:Server Controls (hist | edit) [13,752 bytes] Kulhanek (talk | contribs) (Created page with "Navigation: Documentation / Methods / String Method / STM:Server / STM:Server Controls ---- __NOEDITSECTION__ __NOTOC__")
• 21:0921:09, 2 June 2026 STM::Server Controls (hist | edit) [139 bytes] Kulhanek (talk | contribs) (Created page with "Navigation: Documentation / Methods / String Method / STM:Server / STM:Server Controls ---- __NOEDITSECTION__ __NOTOC__")
• 21:0821:08, 2 June 2026 STM:Server (hist | edit) [158 bytes] Kulhanek (talk | contribs) (Created page with "Navigation: Documentation / Methods / String Method / STM:Client ---- __NOEDITSECTION__ __NOTOC__")
• 20:4020:40, 2 June 2026 Metric Tensor Correction (hist | edit) [74 bytes] Kulhanek (talk | contribs) (Created page with "Navigation: Documentation / Methods / Metric Tensor Correction")
• 18:5118:51, 2 June 2026 STM:Client Controls (hist | edit) [2,209 bytes] Kulhanek (talk | contribs) (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;...")
• 18:4918:49, 2 June 2026 STM:Client (hist | edit) [2,909 bytes] Kulhanek (talk | contribs) (Created page with "Navigation: Documentation / Methods / String Method / STM:Client ---- __NOEDITSECTION__ __NOTOC__")

28 May 2026

• 19:5919:59, 28 May 2026 CV:PTPATHZ (hist | edit) [2,640 bytes] Kulhanek (talk | contribs) (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...")
• 19:5519:55, 28 May 2026 CV:PTPATHS2PN (hist | edit) [3,476 bytes] Kulhanek (talk | contribs) (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...")
• 19:5319:53, 28 May 2026 CV:PTPATHS2P (hist | edit) [2,704 bytes] Kulhanek (talk | contribs) (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...")
• 19:4819:48, 28 May 2026 CV:PTPATHS (hist | edit) [2,243 bytes] Kulhanek (talk | contribs) (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...")
• 19:4619:46, 28 May 2026 PTPATHS (hist | edit) [2,243 bytes] Kulhanek (talk | contribs) (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...")