CamCASP/Notes/3 - Revision history

import>Am592: /* Orient command files for display */

2008-11-25T10:45:18Z

Orient command files for display

@@ Line 343: / Line 343: @@
 Finish
 </pre>
-This is the entire file just so that you can see the entire thing at least once! What have we done? There is a new line in the last section:
+This is the entire file just so that you can see the entire thing at least once! And here is the axis file (see the ORIENT manual for details):
 <pre>
   import file pyridine_Q_ind_2vdW.dat with values

import>Am592: /* Orient command files for display */

2008-11-24T16:09:33Z

Orient command files for display

← Older revision		Revision as of 16:09, 24 November 2008
Line 358:		Line 358:
	</pre>		</pre>
	And if you now run '''ORIENT''' you should get the figure.		And if you now run '''ORIENT''' you should get the figure.
	[[Image:pyridine_Q_ind_saptdft.png\|frame\|right\|Induction map of pyridine with a +1.0 charge calculated using SAPT(DFT) and displayed using ORIENT ]]		[[Image:pyridine_Q_ind_saptdft.png\|thumb\|frame\|right\|Induction map of pyridine with a +1.0 charge calculated using SAPT(DFT) and displayed using ORIENT ]]

import>Am592: /* Orient command files for display */

2008-11-24T16:08:02Z

Orient command files for display

← Older revision		Revision as of 16:08, 24 November 2008
Line 358:		Line 358:
	</pre>		</pre>
	And if you now run '''ORIENT''' you should get the figure.		And if you now run '''ORIENT''' you should get the figure.
			[[Image:pyridine_Q_ind_saptdft.png\|frame\|right\|Induction map of pyridine with a +1.0 charge calculated using SAPT(DFT) and displayed using ORIENT ]]

import>Am592: /* Energy scans for Display using ORIENT */

2008-11-24T15:43:43Z

Energy scans for Display using ORIENT

Show changes

import>Am592: /* Energy scans for Display using ORIENT */

2008-11-07T10:34:28Z

Energy scans for Display using ORIENT

← Older revision		Revision as of 10:34, 7 November 2008
Line 67:		Line 67:
	</pre>		</pre>
	You will see a blob around the molecule. This is OK. Make sure the blob looks roughly like you think it would. There will be no colours. This too is OK. Also, ORIENT will have produced the file		You will see a blob around the molecule. This is OK. Make sure the blob looks roughly like you think it would. There will be no colours. This too is OK. Also, ORIENT will have produced the file
	''pyridine_2vdW.grid'' that contains the grid points and triangles. We need only the grid points. ~~So edit it to comment out the first line which contains the number of points in the grid and delete the list of triangles. Here's what it looks like:~~		''pyridine_2vdW.grid'' that contains the grid points and triangles. We need only the grid points.
			So copy ''pyridine_2vdW.grid'' to ''pyridine_2vdW_points.grid'' and this file as follows:

			1. Comment out the first line which contains the number of points in the grid and

			2. delete the list of triangles.

			Here's what it should look like:
	<pre>		<pre>
			$ more pyridine_2vdW_points.grid
	# 2370 4736		# 2370 4736
	-9.00000000 -1.50000000 -0.63302610		-9.00000000 -1.50000000 -0.63302610

import>Am592 at 18:40, 6 November 2008

2008-11-06T18:40:36Z

New page

[[ CamCASP ]] => [[ CamCASP/Notes | Notes ]] => Energy scans for display

== Energy scans for Display using ORIENT ==

* '''Obtaining the grid'''
ORIENT calculates the surface around the molecule. So we need to setup an ORIENT file to obtain this grid of points. This grid will then be passed to CamCASP which will calculate the interaction energies (next step).

We will use the CLUSTER program to help construct the ORIENT command file.
<pre>
Title Pyridine : properties cluster file

Global
CamCASP /home/ajm/SITUS/current
Units Bohr Degree
Overwrite Yes
End

Molecule pyridine
! Optimzed with PBE0/cc-pVTZ Gaussian03
! C2v symmetry
Units Angstrom
H1 1.0 -2.050322 1.274414 0.000000
H2 1.0 -2.147113 -1.203259 0.000000
H3 1.0 0.000000 -2.487558 0.000000
H4 1.0 2.147113 -1.203259 0.000000
H5 1.0 2.050322 1.274414 0.000000
N 7.0 0.000000 1.382844 0.000000
C1 6.0 -1.134410 0.690452 0.000000
C2 6.0 -1.190513 -0.695795 0.000000
C3 6.0 0.000000 -1.403912 0.000000
C4 6.0 1.190513 -0.695795 0.000000
C5 6.0 1.134410 0.690452 0.000000
End

Files
Molecule pyridine
Basis daTZ
File-prefix pyridine
Orient files for display
Interface file
Memory 2000 MB
End

Finish
</pre>

CLUSTER will create three file. The ''*.template'' file is not needed. You can delete it.

Copy ''pyridine_display.ornt'' to ''pyridine_display_grid.ornt''. Edit ''pyridine_display_grid.ornt'' so that:

1. The radius of any polar hydrogen (one that can participate in an hydrogen-bond) is set to zero. You can do this using
<pre>
Types
Hp Z 1 Radius 0.0
...
End
</pre>
at the start of the file. And in the ''Molecule'' block set all polar hydrogens to ''Type Hp''. For more details please see the ORIENT manual. By the way, you do not need to do this, but doing so makes the scan more true to reality as the distance of close-approach to such hydrogen atoms is smaller than that for other hydrogen atoms.

2. Comment out the statements in the ''Polarizabilities'' block. We will not need polarizabilities to construct the grid.

3. Un-comment the ''Write'' command in the ''Display energy'' block.

Now run ORIENT
<pre>
orient < pyridine_display_grid.ornt
</pre>
You will see a blob around the molecule. This is OK. Make sure the blob looks roughly like you think it would. There will be no colours. This too is OK. Also, ORIENT will have produced the file
''pyridine_2vdW.grid'' that contains the grid points and triangles. We need only the grid points. So edit it to comment out the first line which contains the number of points in the grid and delete the list of triangles. Here's what it looks like:
<pre>
# 2370 4736
-9.00000000 -1.50000000 -0.63302610
-9.00000000 -2.18117397 0.00000000
-9.03969412 -1.50000000 0.00000000
...
... 2370 sets of coordinates...
</pre>

NOTE: By default the surface constructed is the so-called ''2 x vdW'' surface. Basically, double the van der Waals radii of the atoms (except polar hydrogens), stretch a rubber sheet over those spheres, construct the grid of points on the rubber sheet. Well, that's it conceptually. The ORIENT manual has the details. What's important is to realise that you can change the parameters of this surface. For example, you may want a 1.8 x vdW surface. Have a peek in the ''Display energy'' block and tweak the parameters.

* '''CamCASP energy scan'''
Now we need to use this list of points to perform a CamCASP energy scan. Only this scan will be with the molecule (pyridine) and a spherical probe (a neon atom for the dispersion and a +1 charge for the electrostatics and induction). This is not necessary, but is very convenient.

The CamCASP file ''pyridine.cks'' that has been produced by CLUSTER is not in the correct format. We need to add the description of the probe molecule (neon) and the commands for the energy scan.
You will also need to copy the MO and Hessian files for the molecule (pyridine) and neon atom to this directory. I have assumed you have these at hand. If not, calculate them (I'll describe this later)

Copy ''pyridine.cks'' to ''pyridine_scan.cks'' and edit it to look like:
<pre>
TITLE pyridine ... neon / Q energy scan
TITLE Basis d-aug-cc-pVTZ

MEMORY 2454 MB

SET Global_data
CamCASP-path /home/ajm/SITUS/current
Units Bohr cm-1
Scf-code Dalton
XC-func PBE0
Overwrite yes
END

MOLECULE pyridine at 0.0 0.0 0.0
Charge 0
Echo No
Hessian format SAPT2006
MO-file mo-pyridine.data
H1-file h1-pyridine.data
Basis Main
...
End
Basis Aux
...
End
END

Molecule Ne at 0.0 0.0 0.0
Charge 0
Echo No
Hessian format SAPT2006
MO-file mo-ne-daTZ.data
H1-file h1-ne-daTZ.data
Basis Main
Spherical
Units Bohr
Format GAMESS
Ne 10.0 0.00000000 0.00000000 0.00000000 TYPE Ne
#include-camcasp basis/gamess_us/d-aug-cc-pVTZ/Ne
---
End
Basis Aux
Cartesian
Units Bohr
Format TURBOMOLE
Ne 10.0 0.00000000 0.00000000 0.00000000 TYPE Ne
Limit G
#include-camcasp basis/aux/aug-cc-pVQZ/Ne
---
End
End

SET QUAD
Type Gauss-Legendre
Beta 0.5
END

BEGIN DF
Molecule pyridine
Type FULL
Eta = 0.0
Lambda = 0.0
Print only normalization constraints
END
BEGIN DF
Molecule Ne
Type FULL
Eta = 0.0
Lambda = 0.0
Print only normalization constraints
END

SET PROPAGATOR
Type CKS
DF without constraints
DF-integrals
END

Begin Energy-scan
Probe pyridine with Ne and Charge +1.0
Scan E2ind & E2disp & E1elst
Units Bohr
Points
Translations-only
#include pyridine_2vdW_points.grid
End
End

FINISH

</pre>

And I have the MO and Hessian files:
<pre>
ls
h1-ne-daTZ.data pyridine_2vdW.grid pyridine_daTZ_DMA2_L4.mom
h1-pyridine.data pyridine.axes pyridine_display_grid.ornt
mo-ne-daTZ.data pyridine.cks pyridine_display.ornt
mo-pyridine.data pyridine.clt
</pre>

Now we can run CamCASP using
<pre>
runcamcasp pyridine_scan -q intel.q --nochecks
</pre>