## page was renamed from AJMGrpOnly/camcasp/energy-scan-display ## page was renamed from ajm/camcasp/energy-scan-display <> = Energy-Scans for Display = This is meant to be a very specific example of how the ENERGY-SCAN module can be used to generate the data needed to visualise an energy component on [[ajm/camcasp/display|a triangulated surface defined around a molecule]] (though, in principle, something similar should be possible for an atom in a molecule too). == Get the GRID file == First of all, you need to define the surface. This can be done through Orient or [[ajm/camcasp/display|within CamCASP using instructions here.]] {{{#!wiki important Important CamCASP 5.9 and later can generate iso-density grids for the molecule and the atoms-in-the-molecule (the latter using the ISA). }}} == Energy-Scan == Next we need to create a CamCASP command file to perform an energy scan of a molecule with a suitable probe. The idea is to place the probe atom/charge (it must be a spherically symmetrical particle) at each of the points on the triangulated surface, and calculate the required energy at each of those points. To do this, we use the ENERGY-SCAN module like so: {{{ Begin Energy-Scan Scan formamide with Charge +1.0 Energies E1elst Units Bohr Points Translations-Only #include formamide_1.00E-02_iso.grid --- Energy-File formamide_aQZ_iso1.00E-02_Q_elst End }}} In this example, the module is used to calculate the electrostatic energy of the molecule (formamide) with a +1e point charge. The points are read in from file ''formamide_1.00E-02_iso.grid'' which is the output of the DISPLAY module ([[:ajm:camcasp:display|see description here]]). The output will be in a file with prefix ''formamide_aQZ_iso1.00E-02_Q_elst''. There are a few points to note: * ''Translations-Only'' is needed to tell the code that the points are specified as ''Rx Ry Rz'', that is, without any rotation data. This is the appropriate form for spherically symmetric probes like the point charge. * We could have used an atom such as Ne or Cl$^-$ (needs to be closed shell) as a probe. The latter would have been more appropriate if in addition to $E^{(1)}_{\rm elst}$ we also wanted to scan $E^{(2)}_{\rm ind,tot}$ and/or $E^{(2)}_{\rm disp,tot}$. * The file containing the points needs to contain the points only (this will change in CamCASP 5.9). So we need to edit the file ''formamide_1.00E-02_iso.grid'' to comment out or delete the lines that contain text or other information. The edited file will look like: {{{ ! MOL-NAME formamide ! DENSITY-TYPE RHO-C ! UNITS BOHR ! BEGIN SITES ! 1 C 6.00 0.7369 -0.2902 0.0000 ! 2 O 8.00 -0.4197 -2.2642 0.0000 ! 3 N 7.00 -0.3376 2.0382 0.0000 ! 4 H1 1.00 2.8209 -0.2060 0.0000 ! 5 H2 1.00 -2.2333 2.1962 0.0000 ! 6 H3 1.00 0.7228 3.6114 0.0000 ! END SITES ! STEP 0.30000000E+00 ! POINTS 4696 ! TRIANGLES 9388 ! BEGIN DATA -4.2000000 1.2000000 -0.7174596 -4.2358335 1.2000000 -0.6000000 -4.2000000 1.1315009 -0.6000000 -4.2912392 1.2000000 -0.3000000 ... ... 5.5275866 0.0000000 -0.3000000 5.5978608 0.0000000 0.0000000 5.5275828 0.0000000 0.3000000 5.4549442 0.3000000 0.0000000 ! 1 2 3 ! 2 4 5 ! 3 2 5 ! 4 6 7 ! 5 4 7 ! ... ! ... ! 4695 4696 4694 ! 4680 4695 4674 ! 4684 4678 4696 ! 4684 4696 4679 ! END DATA }}} Of course, you could simply delete the commented out lines, but I prefer not to. [[ajm/camcasp/files/formamide-energy-scan-elst|The entire CamCASP command file can be found here.]] == Process the output == ==== Need to convert units? ==== As with any ENERGY-SCAN, pay attention to the units of energy: do you want it to be cm-1 or kJ/mol? Or something else? Of course you can convert units later using the PROCESS code, but it's best to get it right at this stage. Here I've used kJ/mol. To convert units using PROCESS create a file like this: {{{ Global Units kJ/mol End Energy Read formamide_aQZ_iso1.00E-03_Q_elst.dat Write formamide_aQZ_iso1.00E-03_Q_elst_kJ.dat End Finish }}} Call it ''convert_to_kJ.prss'' and run it through PROCESS {{{ $ process < convert_to_kJ.prss }}} ==== Insert data into GRID file ==== Next, to use the results in Orient, you need to insert the energies (in appropriate units) into the grid file. The energies will be in a file called ''formamide_aQZ_iso1.00E-02_Q_elst.dat''. Copy the appropriate column (in this case, the electrostatic energy) and insert it in the original grid file (without any lines deleted or commented out!) to get something like this: {{{ $ more formamide_1.00E-03_iso_aQZ_Q.elst MOL-NAME formamide DENSITY-TYPE RHO-C UNITS BOHR BEGIN SITES 1 C 6.00 0.7369 -0.2902 0.0000 2 O 8.00 -0.4197 -2.2642 0.0000 3 N 7.00 -0.3376 2.0382 0.0000 4 H1 1.00 2.8209 -0.2060 0.0000 5 H2 1.00 -2.2333 2.1962 0.0000 6 H3 1.00 0.7228 3.6114 0.0000 END SITES STEP 0.30000000E+00 POINTS 4696 TRIANGLES 9388 BEGIN DATA -4.2000000 1.2000000 -0.7174596 0.135038E+03 -4.2358335 1.2000000 -0.6000000 0.136834E+03 -4.2000000 1.1315009 -0.6000000 0.134023E+03 -4.2912392 1.2000000 -0.3000000 0.140585E+03 -4.2000000 1.0200695 -0.3000000 0.132162E+03 -4.3095228 1.2000000 0.0000000 0.141816E+03 -4.2000000 0.9819806 0.0000000 0.131182E+03 .... .... 5.6017083 -0.3000000 0.0000000 0.666641E+02 5.5375572 -0.3000000 0.3000000 0.693236E+02 5.5275866 0.0000000 -0.3000000 0.724044E+02 5.5978608 0.0000000 0.0000000 0.693662E+02 5.5275828 0.0000000 0.3000000 0.724046E+02 5.4549442 0.3000000 0.0000000 0.783642E+02 1 2 3 2 4 5 3 2 5 4 6 7 5 4 7 6 8 9 .... .... 4696 4693 4694 4680 4679 4696 4680 4696 4695 4695 4696 4694 4680 4695 4674 4684 4678 4696 4684 4696 4679 END DATA }}} The energies are in the fourth column. The format is {{{ preable ... BEGIN DATA Rx Ry Rz Energy ... i j k <---triangles ... END DATA }}} The UNITS line may not (yet) control the units of the energies. But it will soon. Now the data is ready for use by Orient to visualise the data.