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 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 within CamCASP using instructions here.

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 (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.

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.