Recent changes to Developers.ForceFields.inter

Developers.ForceFields.inter modified by Burkhard Schmidt

Burkhard Schmidt — Fri, 15 Nov 2013 07:25:10 -0000

--- v11
+++ v12
@@ -6,7 +6,7 @@
 Examples
 --------

-* [LJ_12_6 potential for rare gases)](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+ff2/LJ_12_6.m) where the force field is expressed in terms of repulsive (R-12) and attractive (R-6) interactions.
+* [LJ_12_6 potential for rare gases](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+ff2/LJ_12_6.m) where the force field is expressed in terms of repulsive (R-12) and attractive (R-6) interactions.

 * [TIP_3P potential for water](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+ff2/TIP_3P.m) where the force field is expressed in terms Coulomb and Lennard-Jones interactions.

Developers.ForceFields.inter modified by Burkhard Schmidt

Burkhard Schmidt — Thu, 06 Jun 2013 12:14:24 -0000

--- v10
+++ v11
@@ -17,8 +17,8 @@

 * Function header
     function u = myfunction (parameters,q1,q2)
-* function name (here myfunction) is specified as a function handle which is a field of [structured variable intra{*i*}](Developers.Variables.intra) upon [MolDynSim initialization](Users.Programs.mol_Initialize)
+* function name (here myfunction) is specified as a function handle which is a field of [structured variable inter{*i,j*}](Developers.Variables.inter) upon [MolDynSim initialization](Users.Programs.mol_Initialize)
 * input q1: specifies the coordinates of all atoms within the first molecule in a 3*N1 real matrix
 * input q2: specifies the coordinates of all atoms within the second molecule in a 3*N2 real matrix
-* input parameters: a structure containing all parameters necessary for this choice of potential function. It is also set as a field of [structured variable intra{*i*}](Developers.Variables.intra) upon [MolDynSim initialization](Users.Programs.mol_Initialize)
+* input parameters: a structure containing all parameters necessary for this choice of potential function. It is also set as a field of [structured variable inter{*i,j*}](Developers.Variables.inter) upon [MolDynSim initialization](Users.Programs.mol_Initialize)
 * output u: A real number returning the energy in units of kJ/mol.

Developers.ForceFields.inter modified by Burkhard Schmidt

Burkhard Schmidt — Thu, 06 Jun 2013 12:12:19 -0000

--- v9
+++ v10
@@ -6,7 +6,9 @@
 Examples
 --------

-* [TIP3P potential for water](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Demos/H2O/pot_TIP3P.m) where the force field is expressed in terms of the two O-H bond lengths and the H-O-H bond angle.
+* [LJ_12_6 potential for rare gases)](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+ff2/LJ_12_6.m) where the force field is expressed in terms of repulsive (R-12) and attractive (R-6) interactions.
+
+* [TIP_3P potential for water](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+ff2/TIP_3P.m) where the force field is expressed in terms Coulomb and Lennard-Jones interactions.

 * Angle-dependent(!) [DIM potential for molecule-rare gas interaction](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Demos/I2-Kr/pot_DIM_X2_Rg.m) where the force field is expressed in terms of the angle between the X-X bond and the vector connecting to the rare gas atom.

@@ -14,8 +16,8 @@
 -------------

 * Function header
-    function u = pot_myfunction (parameters,q1,q2)
-* function name (here pot_myfunction) is specified as a function handle which is a field of [structured variable intra{*i*}](Developers.Variables.intra) upon [MolDynSim initialization](Users.Programs.mol_Initialize)
+    function u = myfunction (parameters,q1,q2)
+* function name (here myfunction) is specified as a function handle which is a field of [structured variable intra{*i*}](Developers.Variables.intra) upon [MolDynSim initialization](Users.Programs.mol_Initialize)
 * input q1: specifies the coordinates of all atoms within the first molecule in a 3*N1 real matrix
 * input q2: specifies the coordinates of all atoms within the second molecule in a 3*N2 real matrix
 * input parameters: a structure containing all parameters necessary for this choice of potential function. It is also set as a field of [structured variable intra{*i*}](Developers.Variables.intra) upon [MolDynSim initialization](Users.Programs.mol_Initialize)

WikiPage Developers.ForceFields.inter modified by Burkhard Schmidt

Burkhard Schmidt — Mon, 25 Feb 2013 10:22:40 -0000

--- v8
+++ v9
@@ -6,7 +6,7 @@
 Examples
 --------

-* [TIP3P potential for water](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Demos/H2O/pot_TIP3P.m) where the force field is expressed in terms of the I-I bond length.
+* [TIP3P potential for water](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Demos/H2O/pot_TIP3P.m) where the force field is expressed in terms of the two O-H bond lengths and the H-O-H bond angle.

 * Angle-dependent(!) [DIM potential for molecule-rare gas interaction](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Demos/I2-Kr/pot_DIM_X2_Rg.m) where the force field is expressed in terms of the angle between the X-X bond and the vector connecting to the rare gas atom.

WikiPage Developers.ForceFields.inter modified by Burkhard Schmidt

Burkhard Schmidt — Wed, 28 Nov 2012 18:38:35 -0000

WikiPage Developers.ForceFields.inter modified by Burkhard Schmidt

Burkhard Schmidt — Wed, 28 Nov 2012 18:38:24 -0000

--- v6
+++ v7
@@ -8,7 +8,7 @@
 
 * [TIP3P potential for water](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Demos/H2O/pot_TIP3P.m) where the force field is expressed in terms of the I-I bond length.
 
-* Angle-dependent(!) [DIM potential for molecule-rare gas interaction](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Demos/I2-Kr/pot_DIM_X2_Rg) where the force field is expressed in terms of the angle between the X-X bond and the vector connecting to the rare gas atom.
+* Angle-dependent(!) [DIM potential for molecule-rare gas interaction](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Demos/I2-Kr/pot_DIM_X2_Rg.m) where the force field is expressed in terms of the angle between the X-X bond and the vector connecting to the rare gas atom.
 
 MATLAB coding
 -------------

WikiPage Developers.ForceFields.inter modified by Burkhard Schmidt

Burkhard Schmidt — Wed, 28 Nov 2012 18:37:38 -0000

--- v5
+++ v6
@@ -8,14 +8,15 @@
 
 * [TIP3P potential for water](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Demos/H2O/pot_TIP3P.m) where the force field is expressed in terms of the I-I bond length.
 
-* [Angle-dependent(!) potential for iodine-rare gas interaction](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Demos/I2-Kr/pot_) where the force field is expressed in terms of the angle between the I-I bond and the vector connecting to a Kr atom.
+* Angle-dependent(!) [DIM potential for molecule-rare gas interaction](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Demos/I2-Kr/pot_DIM_X2_Rg) where the force field is expressed in terms of the angle between the X-X bond and the vector connecting to the rare gas atom.
 
 MATLAB coding
 -------------
 
 * Function header
-    function u = pot_myfunction (parameters,q)
+    function u = pot_myfunction (parameters,q1,q2)
 * function name (here pot_myfunction) is specified as a function handle which is a field of [structured variable intra{*i*}](Developers.Variables.intra) upon [MolDynSim initialization](Users.Programs.mol_Initialize)
-* input q: specifies the coordinates of all atoms within one molecule in a 3*N real matrix
+* input q1: specifies the coordinates of all atoms within the first molecule in a 3*N1 real matrix
+* input q2: specifies the coordinates of all atoms within the second molecule in a 3*N2 real matrix
 * input parameters: a structure containing all parameters necessary for this choice of potential function. It is also set as a field of [structured variable intra{*i*}](Developers.Variables.intra) upon [MolDynSim initialization](Users.Programs.mol_Initialize)
 * output u: A real number returning the energy in units of kJ/mol.

WikiPage Developers.ForceFields.inter modified by Burkhard Schmidt

Burkhard Schmidt — Wed, 28 Nov 2012 18:34:54 -0000

--- v4
+++ v5
@@ -1,4 +1,21 @@
 Guide on intermolecular force fields in MolDynSim
-========================================
+=================================================
 
-to be written ...
+The intermolecular force field describes the interaction between two molecules (of equal or different chemical species). Typically, these force fields are expressed in terms of distances between pairs of atoms. However, you can feel free to implement also radically different forms of force fields for use in your simulations using MolDynSim.
+
+Examples
+--------
+
+* [TIP3P potential for water](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Demos/H2O/pot_TIP3P.m) where the force field is expressed in terms of the I-I bond length.
+
+* [Angle-dependent(!) potential for iodine-rare gas interaction](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Demos/I2-Kr/pot_) where the force field is expressed in terms of the angle between the I-I bond and the vector connecting to a Kr atom.
+
+MATLAB coding
+-------------
+
+* Function header
+    function u = pot_myfunction (parameters,q)
+* function name (here pot_myfunction) is specified as a function handle which is a field of [structured variable intra{*i*}](Developers.Variables.intra) upon [MolDynSim initialization](Users.Programs.mol_Initialize)
+* input q: specifies the coordinates of all atoms within one molecule in a 3*N real matrix
+* input parameters: a structure containing all parameters necessary for this choice of potential function. It is also set as a field of [structured variable intra{*i*}](Developers.Variables.intra) upon [MolDynSim initialization](Users.Programs.mol_Initialize)
+* output u: A real number returning the energy in units of kJ/mol.

WikiPage Developers.ForceFields.inter modified by Burkhard Schmidt

Burkhard Schmidt — Wed, 28 Nov 2012 13:34:27 -0000

WikiPage Developers.ForceFields.inter modified by Burkhard Schmidt

Burkhard Schmidt — Wed, 28 Nov 2012 13:33:49 -0000