https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.inter/Recent changes to Developers.Variables.interenThu, 20 Jun 2013 13:16:37 -0000https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.inter/<div class="markdown_content"><pre>--- v30 +++ v31 @@ -35,13 +35,13 @@ a | Energy parameter for short range repulsion, in kJ/mol*nm^12 c | Energy parameter for dispersion attraction, in kJ/mol*nm^6 -[@ff2.TIP_4P](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+ff2/TIP_4P.m) | Four-particle model of water: Three Coulomb sites (on H,H,dummy) and one LJ-site (on O atom) +[@ff2.TIP_4P](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+ff2/TIP_4P.m) | [Four-particle model of water](http://dx.doi.org/10.1063/1.445869): Three Coulomb sites (on H,H,dummy) and one LJ-site (on O atom) ---|--- q | Four charges (first one: zero), row vector, in e a | Energy parameter for short range repulsion, in kJ/mol*nm^12 c | Energy parameter for dispersion attraction, in kJ/mol*nm^6 -[@ff2.TIP_5P](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+ff2/TIP_5P.m) | Five-particle model of water: ... to be written ... +[@ff2.TIP_5P](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+ff2/TIP_5P.m) | [Five-particle model of water](http://dx.doi.org/10.1063/1.481505): ... to be written ... ---|--- Warning: | under construction </pre> </div>Burkhard SchmidtThu, 20 Jun 2013 13:16:37 -0000https://sourceforge.net932fea5507e5639284b54a61d95af6096446f15ehttps://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.inter/<div class="markdown_content"><pre>--- v29 +++ v30 @@ -29,7 +29,7 @@ rho | Length parameter for short range repulsion, in nm c_6 | Energy parameter for dispersion attraction, in kJ/mol*nm^6 -[@ff2.TIP_3P](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+ff2/TIP_3P.m) | Three-particle model of water: Three Coulomb sites (on O,H,H) and one LJ-site (on O atom) +[@ff2.TIP_3P](https://sourceforge.net/p/trajlab/moldynsim/code/HEAD/tree/trunk/Sources/+ff2/TIP_3P.m) | [Three-particle model of water](http://dx.doi.org/10.1063/1.445869): Three Coulomb sites (on O,H,H) and one LJ-site (on O atom) ---|--- q | Three charges, row vector, in e a | Energy parameter for short range repulsion, in kJ/mol*nm^12 </pre> </div>Burkhard SchmidtThu, 20 Jun 2013 13:14:57 -0000https://sourceforge.net1c51290c0ea2fa09142c3ee4e5b0e40334984923https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.inter/<div class="markdown_content"><pre>--- v28 +++ v29 @@ -50,9 +50,9 @@ field | description ---|--- -thawed | table of interaction energies between thawed and thawed molecules -frozen1| table of interaction energies between thawed and frozen molecules -frozen2| table of interaction energies between frozen and thawed molecules +thaw_thaw | table of interaction energies between thawed and thawed molecules +thaw_froz | table of interaction energies between thawed and frozen molecules +froz_thaw | table of interaction energies between frozen and thawed molecules Note that these tables are needed for efficient evaluation of gradient and Hessian of the intramolecular force field. Interaction between frozen molecules is disregarded. </pre> </div>Burkhard SchmidtMon, 17 Jun 2013 11:59:10 -0000https://sourceforge.net1ee9b24a7028f8898345ebe06da7c5fdaf80b67dhttps://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.inter/<div class="markdown_content"><pre>--- v27 +++ v28 @@ -54,7 +54,7 @@ frozen1| table of interaction energies between thawed and frozen molecules frozen2| table of interaction energies between frozen and thawed molecules -Note that these tables are needed for efficient evaluation of gradient and Hessian. Interaction between frozen molecules is disregarded. +Note that these tables are needed for efficient evaluation of gradient and Hessian of the intramolecular force field. Interaction between frozen molecules is disregarded. Write your own intermolecular force field: </pre> </div>Burkhard SchmidtMon, 17 Jun 2013 10:27:10 -0000https://sourceforge.net49c2c9f75030fe6e426ca4be91b773d19743cb45https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.inter/<div class="markdown_content"><pre>--- v26 +++ v27 @@ -54,7 +54,8 @@ frozen1| table of interaction energies between thawed and frozen molecules frozen2| table of interaction energies between frozen and thawed molecules -Note that these tables are needed for efficient evaluation of gradient and Hessian ... +Note that these tables are needed for efficient evaluation of gradient and Hessian. Interaction between frozen molecules is disregarded. + Write your own intermolecular force field: ------------------------------------------ </pre> </div>Burkhard SchmidtMon, 10 Jun 2013 10:04:27 -0000https://sourceforge.net838872971e623d88c13c7f635f4d58f28635e43chttps://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.inter/<div class="markdown_content"><pre>--- v25 +++ v26 @@ -50,10 +50,11 @@ field | description ---|--- -thawed | table of interaction energies between thawed and thawed molecules; needed for efficient evaluation of gradient and Hessian +thawed | table of interaction energies between thawed and thawed molecules frozen1| table of interaction energies between thawed and frozen molecules frozen2| table of interaction energies between frozen and thawed molecules +Note that these tables are needed for efficient evaluation of gradient and Hessian ... Write your own intermolecular force field: ------------------------------------------ </pre> </div>Burkhard SchmidtMon, 10 Jun 2013 08:53:50 -0000https://sourceforge.net51443bb93ad161d3d0a4acd906ddf3f86c0966a6https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.inter/<div class="markdown_content"><pre>--- v24 +++ v25 @@ -50,8 +50,9 @@ field | description ---|--- -thawed | table of interaction energies among thawed molecules; needed for efficient evaluation of gradient and Hessian -frozen | table of interaction energies between thawed and frozen molecules +thawed | table of interaction energies between thawed and thawed molecules; needed for efficient evaluation of gradient and Hessian +frozen1| table of interaction energies between thawed and frozen molecules +frozen2| table of interaction energies between frozen and thawed molecules Write your own intermolecular force field: </pre> </div>Burkhard SchmidtMon, 10 Jun 2013 08:52:36 -0000https://sourceforge.net878e84e28c3ef088fb9c07548d10a972c104a39bhttps://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.inter/<div class="markdown_content"><pre>--- v23 +++ v24 @@ -50,6 +50,8 @@ field | description ---|--- +thawed | table of interaction energies among thawed molecules; needed for efficient evaluation of gradient and Hessian +frozen | table of interaction energies between thawed and frozen molecules Write your own intermolecular force field: </pre> </div>Burkhard SchmidtMon, 10 Jun 2013 08:45:31 -0000https://sourceforge.net919a0146baf678b65a476a05b36a6d0b7405bcd2https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.inter/<div class="markdown_content"><pre>--- v22 +++ v23 @@ -1,7 +1,10 @@ Variable "inter{.,.}" in MolDynSim ================================== -This variable characterizes the intermolecular force fields in our simulations, i.e. for interaction between pairs of molecules of (equal and different!) species. It is used in essentially all of the MolDynSim programs. Every entry of the cell matrix is a structured variable that should contain the following two fields: +This variable characterizes the intermolecular force fields in our simulations, i.e. for interaction between pairs of molecules of (equal and different!) species. It is used in essentially all of the MolDynSim programs. Every entry of the cell matrix is a structured variable containing the following items + +Settable parameters +------------------- field | description ---|--- @@ -42,8 +45,14 @@ ---|--- Warning: | under construction +Internal variables +------------------ -Write your own force field: ---------------------------- +field | description +---|--- + + +Write your own intermolecular force field: +------------------------------------------ * If you cannot find a suitable function inside the +ff2 package, you will have to provide one yourself. For a guide how to write an intermolecular force field, please see [here](Developers.ForceFields.inter). </pre> </div>Burkhard SchmidtMon, 10 Jun 2013 08:40:50 -0000https://sourceforge.net18a03518b0c8419ea4e5e2d71ffe89488089621bhttps://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.inter/<div class="markdown_content"><pre>--- v21 +++ v22 @@ -1,7 +1,7 @@ -Variable "inter{i,j}" in MolDynSim +Variable "inter{.,.}" in MolDynSim ================================== -This variable characterizes the intermolecular force fields in our simulations, i.e. for interaction between molecules of *i*-th and *j*-th species. It is used in essentially all of the MolDynSim programs. Every entry*{i,j}* of the cell matrix is a structured variable that should contain the following two fields: +This variable characterizes the intermolecular force fields in our simulations, i.e. for interaction between pairs of molecules of (equal and different!) species. It is used in essentially all of the MolDynSim programs. Every entry of the cell matrix is a structured variable that should contain the following two fields: field | description ---|--- </pre> </div>Burkhard SchmidtMon, 10 Jun 2013 07:14:18 -0000https://sourceforge.net247f0623700b9fcb74908c0dc68ebe26125b3e09