https://sourceforge.net/p/trajlab/moldynsim/wiki/Users.Main/Recent changes to Users.MainenFri, 31 May 2013 10:37:55 -0000https://sourceforge.net/p/trajlab/moldynsim/wiki/Users.Main/<div class="markdown_content"><pre>--- v39 +++ v40 @@ -20,7 +20,7 @@ * [mol_Dynamics](Users.Programs.mol_Dynamics): Numerical solution of equations of motion -* [mol_MonteCarlo](Users.Programs.mol_MonteCarlo): Sampling a canonical distribution +* [mol_MonteCarlo](Users.Programs.mol_MonteCarlo): Sampling a canonical distribution by random walking Advanced techniques for analysis of molecular trajectory data, e.g. geometric and spectral clustering to detect and characterize metastable molecular conformations, can be found in the [MetaStable subproject](http://sf.net/p/trajlab/metastable) </pre> </div>Burkhard SchmidtFri, 31 May 2013 10:37:55 -0000https://sourceforge.net9caa2a7d849bec12c16d18de6f6b9b6cc02b2040https://sourceforge.net/p/trajlab/moldynsim/wiki/Users.Main/<div class="markdown_content"><pre>--- v38 +++ v39 @@ -20,6 +20,8 @@ * [mol_Dynamics](Users.Programs.mol_Dynamics): Numerical solution of equations of motion +* [mol_MonteCarlo](Users.Programs.mol_MonteCarlo): Sampling a canonical distribution + Advanced techniques for analysis of molecular trajectory data, e.g. geometric and spectral clustering to detect and characterize metastable molecular conformations, can be found in the [MetaStable subproject](http://sf.net/p/trajlab/metastable) General remarks </pre> </div>Burkhard SchmidtThu, 30 May 2013 18:10:52 -0000https://sourceforge.neta47e41d466f7d72ffed45f087d2dcaa868bcd5b1https://sourceforge.net/p/trajlab/moldynsim/wiki/Users.Main/<pre>--- v37 +++ v38 @@ -8,17 +8,17 @@ The MATLAB functions comprising the MolDynSim package are listed in the following: -* [MolDynSim initialization](Users.Programs.mol_init): Set force field parameters and initial values for all MolSim programs +* [mol_Initialize](Users.Programs.mol_Initialize): Set force field parameters and initial values for all MolSim programs -* [Scan of force field](Users.Programs.mol_scan_1D): Scan force field along specified direction +* [mol_ScanPot_1D](Users.Programs.mol_ScanPot_1D): Scan force field along specified direction -* [Geometry optimization](Users.Programs.mol_opt): Find minimum energy conformations of a molecular system +* [mol_Optimize](Users.Programs.mol_Optimize): Find minimum energy conformations of a molecular system -* [Sorting minima](Users.Programs.mol_sort): Sort minima stored in XYZ-files according to increasing energy +* [mol_SortMinima](Users.Programs.mol_SortMinima): Sort minima stored in XYZ-files according to increasing energy -* [Normal mode analysis](Users.Programs.mol_vib): Find frequencies and spatial patterns of molecular vibrations +* [mol_Vibrations](Users.Programs.mol_Vibrations): Find frequencies and spatial patterns of molecular vibrations -* [Molecular dynamics simulations](Users.Programs.mol_dyn): Numerical solution of equations of motion +* [mol_Dynamics](Users.Programs.mol_Dynamics): Numerical solution of equations of motion Advanced techniques for analysis of molecular trajectory data, e.g. geometric and spectral clustering to detect and characterize metastable molecular conformations, can be found in the [MetaStable subproject](http://sf.net/p/trajlab/metastable) </pre>Burkhard SchmidtFri, 23 Nov 2012 13:54:25 -0000https://sourceforge.net7e22564e55c6f78480d20fcacbe9d3819aca2930https://sourceforge.net/p/trajlab/moldynsim/wiki/Users.Main/<pre>--- v36 +++ v37 @@ -20,6 +20,8 @@ * [Molecular dynamics simulations](Users.Programs.mol_dyn): Numerical solution of equations of motion +Advanced techniques for analysis of molecular trajectory data, e.g. geometric and spectral clustering to detect and characterize metastable molecular conformations, can be found in the [MetaStable subproject](http://sf.net/p/trajlab/metastable) + General remarks --------------- </pre>Burkhard SchmidtThu, 22 Nov 2012 19:08:12 -0000https://sourceforge.net00a0352ffae06aa8b3bdfd052e12643c3faca0a3https://sourceforge.net/p/trajlab/moldynsim/wiki/Users.Main/<pre>--- v35 +++ v36 @@ -3,8 +3,8 @@ The MolDynSim software (which is a part of the [TrajLab project](https://sourceforge.net/p/trajlab)) can be used for molecular simulations involving an arbitrary number of molecular species, number of molecules per species, number of atoms per molecule and number of spatial degrees of freedom. It is based on the notion of intra- and/or intermolecular force fields (alias potential energy functions) which can be freely defined by the user. For technical details see the [respective chapter of the developers' guide](Developers.ForceFields.Main). Along with the gradient (vector) as well as the Hessian (matrix), the implementation and characterization of an appropriate force field is the central task in every MolDynSim simulation. -Programs/scripts ----------------- +Programs +-------- The MATLAB functions comprising the MolDynSim package are listed in the following: </pre>Burkhard SchmidtWed, 21 Nov 2012 19:38:06 -0000https://sourceforge.netd134c58981f243305e05d1247a552270e5ac3f45https://sourceforge.net/p/trajlab/moldynsim/wiki/Users.Main/<pre>--- v34 +++ v35 @@ -1,8 +1,7 @@ MolDynSim Users' guide ====================== -The MolDynSim software (which is a part of the [TrajLab project](https://sourceforge.net/p/trajlab)) can be used for molecular simulations involving an arbitrary number of molecular species, numbre of molecules per species, and number of atoms per molecule. It is based on the notion of intra- and/or intermolecular force fields (alias potential energy functions) which can be freely defined by the user. For technical details see the [respective chapter of the developers' guide](Developers.ForceFields.Main). Along with the gradient (vector) as well as the Hessian (matrix), the implementation and characterization of an appropriate force field is the central task in every MolDynSim simulation - +The MolDynSim software (which is a part of the [TrajLab project](https://sourceforge.net/p/trajlab)) can be used for molecular simulations involving an arbitrary number of molecular species, number of molecules per species, number of atoms per molecule and number of spatial degrees of freedom. It is based on the notion of intra- and/or intermolecular force fields (alias potential energy functions) which can be freely defined by the user. For technical details see the [respective chapter of the developers' guide](Developers.ForceFields.Main). Along with the gradient (vector) as well as the Hessian (matrix), the implementation and characterization of an appropriate force field is the central task in every MolDynSim simulation. Programs/scripts ---------------- </pre>Burkhard SchmidtMon, 19 Nov 2012 13:59:01 -0000https://sourceforge.net24a4728c2595553886e3b171983bfe6c83294580https://sourceforge.net/p/trajlab/moldynsim/wiki/Users.Main/<pre>--- v33 +++ v34 @@ -33,4 +33,4 @@ Visualization -------------- -Although there are some rudimentary fragments of MATLAB-based molecular visualization codes in the repository at SourceForge ('OldStuff'), it is recommended to use external codes for molecular visualization which should be interfaced through the XYZ files produced by our MolDynSim codes. Our recommendation is to use the [VMD program](http://www.ks.uiuc.edu/Research/vmd) which is highly flexible and available (free of charge!) for all major computing platforms (Windows, Linux, MacOS). VMD is being developed by Prof. Klaus Schulten's group at University of Illinois, Urbana, Champaign. Alternatively, you can use [JMOL](http://jmol.sourceforge.net) which is an open source molecule viewer written in Java. It runs as a standalone application and as a web browser applet. +Although there are some rudimentary fragments of MATLAB-based molecular visualization codes in the repository at SourceForge ('OldStuff'), it is recommended to use external codes for molecular visualization which should be interfaced through the XYZ files produced by our MolDynSim codes. Our recommendation is to use the [VMD program](http://www.ks.uiuc.edu/Research/vmd) which is highly flexible and available (free of charge!) for all major computing platforms (Windows, Linux, MacOS). VMD is being developed by [Prof. Klaus Schulten's group](http://www.ks.uiuc.edu) at University of Illinois, Urbana, Champaign. Alternatively, you can use [JMOL](http://jmol.sourceforge.net) which is an open source molecule viewer written in Java. It runs as a standalone application and as a web browser applet. </pre>Burkhard SchmidtFri, 16 Nov 2012 14:18:27 -0000https://sourceforge.netc63fbae68a03e01fd37843ca6aa551a528d84790https://sourceforge.net/p/trajlab/moldynsim/wiki/Users.Main/<pre>--- v32 +++ v33 @@ -33,4 +33,4 @@ Visualization -------------- -Although there are some rudimentary fragments of MATLAB-based molecular visualization codes in the repository at SourceForge, it is recommended to use external codes for molecular visualization which should be interfaced through the XYZ files produced by our MolDynSim codes. Our recommendation is to use the [VMD program](http://www.ks.uiuc.edu/Research/vmd) which is highly flexible and available (free of charge!) for all major computing platforms (Windows, Linux, MacOS). VMD is being developed by Prof. Klaus Schulten's group at University of Illinois, Urbana, Champaign. Alternatively, you can use [JMOL](http://jmol.sourceforge.net) which is an open source molecule viewer written in Java. It runs as a standalone application and as a web browser applet. +Although there are some rudimentary fragments of MATLAB-based molecular visualization codes in the repository at SourceForge ('OldStuff'), it is recommended to use external codes for molecular visualization which should be interfaced through the XYZ files produced by our MolDynSim codes. Our recommendation is to use the [VMD program](http://www.ks.uiuc.edu/Research/vmd) which is highly flexible and available (free of charge!) for all major computing platforms (Windows, Linux, MacOS). VMD is being developed by Prof. Klaus Schulten's group at University of Illinois, Urbana, Champaign. Alternatively, you can use [JMOL](http://jmol.sourceforge.net) which is an open source molecule viewer written in Java. It runs as a standalone application and as a web browser applet. </pre>Burkhard SchmidtFri, 16 Nov 2012 14:06:59 -0000https://sourceforge.net47bf280a1634de257499b37577d5610a94374e16https://sourceforge.net/p/trajlab/moldynsim/wiki/Users.Main/<pre>--- v31 +++ v32 @@ -33,4 +33,4 @@ Visualization -------------- -Although there are some rudimentary fragments of MATLAB-based molecular visualization codes in the repository at SourceForge, it is recommended to use external codes for molecular visualization which should be interfaced through the XYZ files produced by our MolDynSim codes. Our recommendation is to use the [VMD program](http://www.ks.uiuc.edu/Research/vmd) which is highly flexible and available (free of charge!) for all major computing platforms (Windows, Linux, MacOS). VMD is being developed by Prof. Klaus Schulten's group at University of Illinois, Urbana, Champaign. +Although there are some rudimentary fragments of MATLAB-based molecular visualization codes in the repository at SourceForge, it is recommended to use external codes for molecular visualization which should be interfaced through the XYZ files produced by our MolDynSim codes. Our recommendation is to use the [VMD program](http://www.ks.uiuc.edu/Research/vmd) which is highly flexible and available (free of charge!) for all major computing platforms (Windows, Linux, MacOS). VMD is being developed by Prof. Klaus Schulten's group at University of Illinois, Urbana, Champaign. Alternatively, you can use [JMOL](http://jmol.sourceforge.net) which is an open source molecule viewer written in Java. It runs as a standalone application and as a web browser applet. </pre>Burkhard SchmidtFri, 16 Nov 2012 13:45:43 -0000https://sourceforge.net4c6db7dcbf769580e01df9c6564086087561e219https://sourceforge.net/p/trajlab/moldynsim/wiki/Users.Main/<pre>--- v30 +++ v31 @@ -7,7 +7,7 @@ Programs/scripts ---------------- -The MATLAB scripts comprising the MolDynSim package are listed in the following: +The MATLAB functions comprising the MolDynSim package are listed in the following: * [MolDynSim initialization](Users.Programs.mol_init): Set force field parameters and initial values for all MolSim programs @@ -24,7 +24,7 @@ General remarks --------------- -* Note that all MolDynSim programs use [molecular units](Users.Molecular Units) throughout. +* Note that all MolDynSim functions use [molecular units](Users.Molecular Units) throughout. * For a quick start of your projects using MolDynSim, see our [demo examples](Demos.Main). </pre>Burkhard SchmidtFri, 16 Nov 2012 13:32:59 -0000https://sourceforge.net1b7b67abae19bc2372eb3f9403d79382ac575e52