paraTypeCharmm: indicates whether or not the parameter file is in the format used by the CHARMM force field.For instance, if a previous simulation ended at time step 552, the command firsttimestep 553 would be used.ĥ The ``Simulation Parameters" section contains many commands, commented into different categories: It is typically useful when restarting a simulation. firsttimestep: simply sets a number value for the first time step of the simulation.If you place the text `` $outputname" in the configuration file, NAMD simply reads it as a label for `` ubq_ws_eq". set outputname: creates a variable called ``outputname" in which to store a generic name for output files.(Creating variables is useful since you can alter the value of that variable in a single place if it is listed many times in the configuration file.) If you place the text `` $temperature" in the configuration file, NAMD simply reads it as a label for the number `` 310". set temperature: creates a variable called ``temperature" in which to store a value for the initial temperature of the system.coordinates: calls the initial coordinate data from the file listed next to it (in this case.structure: calls the psf file describing the system (.Your comment should readĤ The ``Adjustable Parameters" section contains five commands: In the middle of a line, `` #" is used to comment out the remainder of the line.ģ The ``Job Description" section contains only comments, and its purpose is to inform those who view the configuration file about what it is meant for. Note that when ``#" appears at the beginning of a line, the entire line is treated as a comment and ignored by NAMD. The configuration file may seem complex at first, but it will be examined line by line to determine its function in your simulation. The pdb, psf, and parameter files, which may be used by many other simulations, are placed in your common directory and are called by each respective configuration file.Ģ Open the configuration file, ubq_ws_eq.conf by typing nedit ubq_ws_eq.conf. The configuration file is the only input file placed here, since it is particular to this simulation. Here, you will find a configuration file for the minimization and equilibration of ubiquitin in a water sphere.Īll output files for the minimization and equilibration of your ubiquitin in a water sphere system will be placed in this directory. It must be inserted just before the End grid generation command.1 Go to your 1-2-sphere directory by typing cd. Transforms the current mesh from a spherical coordinate system into a planar 2-D system. The input data for this instruction is identical to that required for the Project 2d grid instruction described above. It must be inserted just before the End grid generation command. Transforms the current mesh from a planar 2-D coordinate system into a spherical system. The input data for this instruction is identical to that required for the Project grid instruction described above. The map of Canada now shows much less distortion but the elements are deformed The map of Canada is shown as a referenceįigure 5.6: Mesh using Albers Equal-area Projection. The grid produced by the Generate blocks interactive instruction is shown on Figure 5.5 and once projected, the grid looks like the one on Figure 5.6:įigure 5.5: Mesh in Geographic Coordinates (lat/long). Generate blocks interactive grade x - 150 - 50 5 1 5 grade y 40 85 5 1 5 grade z 0 10 10 1 10 end project grid albers equal - area - 100 60 ! projection origin 55 70 ! standard parallels 1 ! 1=sphere, 2=ellipsoid end The following example uses the Project Grid instruction: Transforms the current mesh from a spherical system into a planar 2-D coordinate system. Acceptable values for the variable datum are: (b) datum The datum used for the projection. For the Lambert projection, the following additional data are required: (a) lon0, lat0 The longitude and latitude for the origin of the projection. Acceptable values for the variable datum are:ġ Sphere. (c) datum The datum used for the projection. (b) lat1, lat2 The latitude of the standard parallels. (a) lon0, lat0 The longitude and latitude for the origin of the projection. For the Albers projection, the following additional data are required: Currently, the only valid inputs for projt are albers equal-area or lambert azimuthal equal-area, which apply the Albers conical or Lambert azimuthal equal-area projections respectively. projt The projection type to be applied.The following command can be used to correct the distortion which occurs when modelling large continental scale problems. Figure 5.5 illustrates the degree of distortion that can occur (which is especially severe at the poles) when a spherical geographic coordinate system, such as longitude and latitude, is mapped directly into a planar 2-D coordinate system.
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