https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics/Recent changes to Developers.Variables.dynamicsenFri, 07 Jun 2013 11:04:25 -0000https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics/<div class="markdown_content"><pre>--- v17 +++ v18 @@ -34,5 +34,6 @@ field | description ---|--- -mc.handle | variants of Monte Carlo algorithm (Matlab function handle). See here for a [list of available random walkers](https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics.mc) temperature | desired value of temperature (real positive number in Kelvin units); governs acceptance/rejection of steps in random walk +mc.handle | variants of Monte Carlo algorithm (Matlab function handle). See here for a [list of available random walkers](https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics.mc) +temperature | desired value of temperature (real positive number in Kelvin units); governs acceptance/rejection of steps in random walk mc.delta | max. size of steps in random walk </pre> </div>Burkhard SchmidtFri, 07 Jun 2013 11:04:25 -0000https://sourceforge.net9778f203776884fe0326badf731b01ebe43f6547https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics/<div class="markdown_content"><pre>--- v16 +++ v17 @@ -25,7 +25,7 @@ field | description ---|--- -mc.handle | choice of "thermostat" algorithm (Matlab function handle). See here for a [list of available thermostats](https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics.tmp) +tmp.handle | choice of "thermostat" algorithm (Matlab function handle). See here for a [list of available thermostats](https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics.tmp) temperature | desired value of temperature (real positive number in Kelvin units); is achieved by using a "thermostat". </pre> </div>Burkhard SchmidtFri, 07 Jun 2013 11:03:49 -0000https://sourceforge.neta25bb16ade6f6f86d13fa8ed9754f81eff0d881dhttps://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics/<div class="markdown_content"><pre>--- v15 +++ v16 @@ -5,10 +5,10 @@ field | description ---|--- -propa_handle| choose propagator for positions/velocities (MATLAB function handle). See here for a [list of available propagators/integrators](https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics.md) +md.handle| choose propagator for positions/velocities (MATLAB function handle). See here for a [list of available propagators/integrators](https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics.md) n_step | number of steps to be simulated (positive integer) n_save | number of steps between saves (positive integer); use this to limit the size of the resulting trajectory files -t_step| size of time step (positive real number, in ps units) +t_step| size of time step (positive real number, in ps units, MD only) seed | seed generation of random numbers; used for initial velocities (integer); use this to create reproducible sequences of random numbers ensemble | choose thermodynamic ensemble, e. g., 'NVE', 'NVT' (three letter code). Not required for MonteCarlo which does NVT always. @@ -25,17 +25,14 @@ field | description ---|--- +mc.handle | choice of "thermostat" algorithm (Matlab function handle). See here for a [list of available thermostats](https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics.tmp) temperature | desired value of temperature (real positive number in Kelvin units); is achieved by using a "thermostat". -thermo_handle | choice of "thermostat" algorithm (Matlab function handle). See here for a [list of available thermostats](https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics.tmp) -thermo_couple | Time constant of thermostat (real number in ps units) + Monte Carlo NVT simulations only -------------------------------- field | description ---|--- -temperature | desired value of temperature (real positive number in Kelvin units); governs acceptance/rejection of steps in random walk -mc_delta | max. size of steps in random walk -mc_handle | variants of Monte Carlo algorithm (Matlab function handle). See here for a [list of available random walkers](https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics.mc) -mc_adjust | how often to adjust temperature (simulated annealing only) -mc_factor | adjusting factor for temperature (simulated annealing only) +mc.handle | variants of Monte Carlo algorithm (Matlab function handle). See here for a [list of available random walkers](https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics.mc) temperature | desired value of temperature (real positive number in Kelvin units); governs acceptance/rejection of steps in random walk +mc.delta | max. size of steps in random walk </pre> </div>Burkhard SchmidtFri, 07 Jun 2013 11:01:38 -0000https://sourceforge.net0603279dcd92aa3798c4ca0daa0f6ab7788c12f9https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics/<div class="markdown_content"><pre>--- v14 +++ v15 @@ -5,7 +5,7 @@ field | description ---|--- -propa_handle| choose propagator for positions/velocities (MATLAB function handle) +propa_handle| choose propagator for positions/velocities (MATLAB function handle). See here for a [list of available propagators/integrators](https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics.md) n_step | number of steps to be simulated (positive integer) n_save | number of steps between saves (positive integer); use this to limit the size of the resulting trajectory files t_step| size of time step (positive real number, in ps units) @@ -25,8 +25,8 @@ field | description ---|--- -temperature | desired value of temperature (real positive number in Kelvin units); is achieved by using a "thermostat", see below -thermo_handle | choice of "thermostat" algorithm (Matlab function handle) +temperature | desired value of temperature (real positive number in Kelvin units); is achieved by using a "thermostat". +thermo_handle | choice of "thermostat" algorithm (Matlab function handle). See here for a [list of available thermostats](https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics.tmp) thermo_couple | Time constant of thermostat (real number in ps units) Monte Carlo NVT simulations only @@ -36,6 +36,6 @@ ---|--- temperature | desired value of temperature (real positive number in Kelvin units); governs acceptance/rejection of steps in random walk mc_delta | max. size of steps in random walk -mc_handle | variants of Monte Carlo algorithm (Matlab function handle): 'mc_multi', 'mc_single', 'mc_anneal' +mc_handle | variants of Monte Carlo algorithm (Matlab function handle). See here for a [list of available random walkers](https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics.mc) mc_adjust | how often to adjust temperature (simulated annealing only) mc_factor | adjusting factor for temperature (simulated annealing only) </pre> </div>Burkhard SchmidtFri, 07 Jun 2013 08:06:28 -0000https://sourceforge.net394aa87b627c49e5f860a425a6b744791f2d136chttps://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics/<div class="markdown_content"><pre>--- v13 +++ v14 @@ -37,3 +37,5 @@ temperature | desired value of temperature (real positive number in Kelvin units); governs acceptance/rejection of steps in random walk mc_delta | max. size of steps in random walk mc_handle | variants of Monte Carlo algorithm (Matlab function handle): 'mc_multi', 'mc_single', 'mc_anneal' +mc_adjust | how often to adjust temperature (simulated annealing only) +mc_factor | adjusting factor for temperature (simulated annealing only) </pre> </div>Burkhard SchmidtFri, 31 May 2013 17:32:18 -0000https://sourceforge.net637faddb6383f141a8338278ea4f42856b7efbf0https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics/<div class="markdown_content"><pre>--- v12 +++ v13 @@ -10,35 +10,30 @@ n_save | number of steps between saves (positive integer); use this to limit the size of the resulting trajectory files t_step| size of time step (positive real number, in ps units) seed | seed generation of random numbers; used for initial velocities (integer); use this to create reproducible sequences of random numbers -ensemble | choose thermodynamic ensemble, e. g., 'NVE', 'NVT' (three letter code) +ensemble | choose thermodynamic ensemble, e. g., 'NVE', 'NVT' (three letter code). Not required for MonteCarlo which does NVT always. -NVE simulations only -==================== -e_total -------- -* desired value of total energy, achieved by scaling of initial velocities -* example: -05 (real number in kJ/mol units) should be *above* global minimum of force field :-) +Molecular dynamics NVE simulations only +--------------------------------------- -perturb -------- -* random perturbation of initial coordinates -* example: 0.01 (real number in nm units) +field | description +---|--- +e_total | desired value of total energy, achieved by scaling of initial velocities (real number in kJ/mol units) should be *above* global minimum of force field :-) +perturb | random perturbation of initial coordinates (real number in nm units) -NVT simulations only -==================== +Molecular dynamics NVT simulations only +--------------------------------------- -temperature ------------ -* desired value of temperature -* example: 30 (real positive number in Kelvin units) -* can be achieved by using a "thermostat", see below +field | description +---|--- +temperature | desired value of temperature (real positive number in Kelvin units); is achieved by using a "thermostat", see below +thermo_handle | choice of "thermostat" algorithm (Matlab function handle) +thermo_couple | Time constant of thermostat (real number in ps units) -thermo_handle -------------- -* choice of "thermostat" algorithm -* example: @dyn_berendsen (function handle) +Monte Carlo NVT simulations only +-------------------------------- -thermo_couple -------------- -* Time constant of thermostat -* example: 001 (real number in ps units) +field | description +---|--- +temperature | desired value of temperature (real positive number in Kelvin units); governs acceptance/rejection of steps in random walk +mc_delta | max. size of steps in random walk +mc_handle | variants of Monte Carlo algorithm (Matlab function handle): 'mc_multi', 'mc_single', 'mc_anneal' </pre> </div>Burkhard SchmidtFri, 31 May 2013 17:29:59 -0000https://sourceforge.net6060d93eeb240a31ee02cc9b72cfe39cee71206chttps://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics/<div class="markdown_content"><pre>--- v11 +++ v12 @@ -9,16 +9,8 @@ n_step | number of steps to be simulated (positive integer) n_save | number of steps between saves (positive integer); use this to limit the size of the resulting trajectory files t_step| size of time step (positive real number, in ps units) -seed ----- -* seed generation of random numbers; used for initial velocities -* example: 42 (integer) -* use this to create reproducible sequences of random numbers - -ensemble --------- -* choose thermodynamic ensemble -* example: 'NVE'|'NVT' (three letter code) +seed | seed generation of random numbers; used for initial velocities (integer); use this to create reproducible sequences of random numbers +ensemble | choose thermodynamic ensemble, e. g., 'NVE', 'NVT' (three letter code) NVE simulations only ==================== </pre> </div>Burkhard SchmidtFri, 31 May 2013 12:35:08 -0000https://sourceforge.net7b914e8b1e2228682d85d9e7139fe13ffea24b88https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics/<div class="markdown_content"><pre>--- v10 +++ v11 @@ -1,31 +1,14 @@ Variable "dynamics" in MolDynSim ================================== -This variable specifies details of the molecular dynamics (trajectory) simulations in our [mol_Dynamics.m](Users.Programs.mol_Dynamics) MATLAB function. It is a structured variable that should initially containing the following fields : +This variable specifies details of the molecular dynamics (trajectory) simulations in our [mol_Dynamics.m](Users.Programs.mol_Dynamics) and/or [mol_MonteCarlo.m](Users.Programs.mol_MonteCarlo) MATLAB function. It is a structured variable that should initially containing the following fields : -propa_handle ------------- -* choose propagator for positions/velocities -* example: @dyn_vel_verlet (function handle) here: velocity Verlet method - -n_step ------- -* number of time steps to be simulated -* example: 2000 (integer) - -n_save ------- -* number of time steps between saves -* example: 050 (positive integer number) -* use this to limit the size of the resulting trajectory files - -t_step ------- -* size of time step -* example: 0.001 (positive real number, in ps units) here 0.001 ps = 1fs -* keep small enough to guarantee precision -* but not smaller than necessary to guarantee efficiency - +field | description +---|--- +propa_handle| choose propagator for positions/velocities (MATLAB function handle) +n_step | number of steps to be simulated (positive integer) +n_save | number of steps between saves (positive integer); use this to limit the size of the resulting trajectory files +t_step| size of time step (positive real number, in ps units) seed ---- * seed generation of random numbers; used for initial velocities </pre> </div>Burkhard SchmidtFri, 31 May 2013 12:29:30 -0000https://sourceforge.net3ca9b0f70b98f6ff87a2e771f03ffef08c50a52bhttps://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics/<pre>--- v9 +++ v10 @@ -16,13 +16,13 @@ n_save ------ * number of time steps between saves -* example: 050 (integer) +* example: 050 (positive integer number) * use this to limit the size of the resulting trajectory files t_step ------ -* size of time step in ps -* example: 0.001 (real) here 0.001 ps = 1fs +* size of time step +* example: 0.001 (positive real number, in ps units) here 0.001 ps = 1fs * keep small enough to guarantee precision * but not smaller than necessary to guarantee efficiency @@ -30,6 +30,7 @@ ---- * seed generation of random numbers; used for initial velocities * example: 42 (integer) +* use this to create reproducible sequences of random numbers ensemble -------- @@ -38,12 +39,31 @@ NVE simulations only ==================== -e_total = -05; % for NVE: total energy [kJ/mol] -perturb = 0.01; % for NVE: random perturbation [nm] +e_total +------- +* desired value of total energy, achieved by scaling of initial velocities +* example: -05 (real number in kJ/mol units) should be *above* global minimum of force field :-) + +perturb +------- +* random perturbation of initial coordinates +* example: 0.01 (real number in nm units) NVT simulations only ==================== -temperature = 30; % for NVT: temperature [Kelvin] -seed = 42; % for NVT: seed random numbers -thermo_handle = @dyn_berendsen; % choose Berensen thermostat -thermo_couple = 001; % Time constant of thermostat [ps] + +temperature +----------- +* desired value of temperature +* example: 30 (real positive number in Kelvin units) +* can be achieved by using a "thermostat", see below + +thermo_handle +------------- +* choice of "thermostat" algorithm +* example: @dyn_berendsen (function handle) + +thermo_couple +------------- +* Time constant of thermostat +* example: 001 (real number in ps units) </pre>Burkhard SchmidtWed, 28 Nov 2012 09:58:28 -0000https://sourceforge.net9fd7a3616a3789e22c23a103f49ddc8ae7edc415https://sourceforge.net/p/trajlab/moldynsim/wiki/Developers.Variables.dynamics/<pre>--- v8 +++ v9 @@ -5,33 +5,36 @@ propa_handle ------------ -* example: @dyn_vel_verlet * choose propagator for positions/velocities +* example: @dyn_vel_verlet (function handle) here: velocity Verlet method n_step ------ +* number of time steps to be simulated * example: 2000 (integer) -* number of time steps n_save ------ +* number of time steps between saves * example: 050 (integer) -* number of time steps between saves +* use this to limit the size of the resulting trajectory files t_step ------ +* size of time step in ps * example: 0.001 (real) here 0.001 ps = 1fs -* size of time step in ps +* keep small enough to guarantee precision +* but not smaller than necessary to guarantee efficiency seed ---- +* seed generation of random numbers; used for initial velocities * example: 42 (integer) -* seed generation of random numbers; used for initiaL velocities ensemble -------- -* example: 'NVE' NVE/NVT * choose thermodynamic ensemble +* example: 'NVE'|'NVT' (three letter code) NVE simulations only ==================== </pre>Burkhard SchmidtWed, 28 Nov 2012 09:46:13 -0000https://sourceforge.netb5523c5a371babbeb24f0d3abc67cf91ccd7735c