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Using DMACRYS and
NEIGHCRYS
The new programmes, NEIGHCRYS and DMACRYS, can be used for larger systems
than were previsouly possible with DMAREL and Neighbours. This is because
of the new numbering system used. The codes can also use a wider range
of potentials - either user-defined or, more significantly, the Williams
01 potentials [Williams, D.E., J. Comp. Chem (2001)], where the implicite
foreshortening of distances to hydrogen is dealt with.
Here is an outline of how to use the new codes in the following sections:
- General notes on the new codes
- Changes to the labelling and file contents (fort.21,
fort.12, mol.geom, dmarel.axis, fit.pots, bondlengths)
- How to do a proper Williams run (for a single res file)
- How to do a ‘wrong’ Williams run
- How to do an old FIT run
1. General notes on the new codes
The main feature of the new codes is that a greter number of atoms can
be used - up to 99999 atoms in total may be present in the unit cell.
This has necessitated a change in the atom labelling used, which means
that all files are a different format.
The new utility programme NEIGHCRYS will correctly generate the .dmain
file from your starting files.
DMACRYS is also able to calculate the properties using the same programme
(for DMAREL, you used to use DMAREL3.11 for the properties calculation),
and pressure can be introduced into the system.
2. Changes to the labelling and file contents
(fort.21, fort.12, mol.geom, dmarel.axis, fit.pots, bondlengths)
Labels
The atom labelling system has changed since the last version of DMAREL
was released.
The atoms are labelled C_F1_1___1___ . The underscores are
essential, and the label is broken down like this:
C_ : The first two characters in the label are the atom type.
If there is only letter in the label, the blank is filled with an underscore.
E.g. C_ ,O_ ,N_, H_, Br, Cl, etc. Note that these labels are case sensitive.
This means that is the SFAC line of your .res file (where NEIGHCRYS reads
the atoms types in) the first letter must be capital and the second small.
F1 : The next two characters are the potential type. These
are assigned automatically, but you should check
them manually. If you are using FIT, the types are all F1, except
the hydrogens which may be F2 or F3.
_ : The next character is a flag. This is blank, unless the
atom is in a moleucle that has been inverted by NEIGHCRYS, in which case
it is I.
1____ : The next 5 characters are the atom number in the
molecule. Numbering restarts for each atom type, i.e. all carbon atoms
are labelled 1-5 (say), then nitrogen 1-2, oxygen 1-2 and hydrogen 1-8
(see pasted text below) This completes the short
atom label.
1____ : The last 5 characters complete the full
atom label. This identifies the atom number in the unit cell, and
sets the limit of the maximum number of atoms in the cell to 99999. (see
pasted text below)
These atom labels will infiltrate many of the files. You can find these
labels in fort.21. To generate them, run NEIGHCRYS with only the basic
files – your .res file, a potential file, and bondlengths. NB:
The bondlengths file must have the atom labels changed from CAR to C_
etc.
This will generate a list of atom types in your fort.21 file that looks
like this:
Equivalent basis atoms
atom atomic name input molecule invert
index number name number flag
1 6 C_F1_1____1____ C1 1 F
2 6 C_F1_1____15___ 2 F
3 6 C_F1_2____2____ C2 1 F
4 6 C_F1_2____16___ 2 F
5 8 O_F1_1____3____ O1 1 F
6 8 O_F1_1____17___ 2 F
7 8 O_F1_2____4____ O2 1 F
8 8 O_F1_2____18___ 2 F
9 7 N_F1_1____5____ N1 1 F
10 7 N_F1_1____19___ 2 F
11 7 N_F1_2____6____ N2 1 F
12 7 N_F1_2____20___ 2 F
13 7 N_F1_3____7____ N3 1 F
14 7 N_F1_3____21___ 2 F
15 7 N_F1_4____8____ N4 1 F
16 7 N_F1_4____22___ 2 F
17 1 H_F2_1____9____ H1 1 F
18 1 H_F2_1____23___ 2 F
19 1 H_F2_2____10___ H2 1 F
20 1 H_F2_2____24___ 2 F
21 1 H_F2_3____11___ H3 1 F
22 1 H_F2_3____25___ 2 F
23 1 H_F2_4____12___ H4 1 F
24 1 H_F2_4____26___ 2 F
25 1 H_F2_5____13___ H5 1 F
26 1 H_F2_5____27___ 2 F
27 1 H_F2_6____14___ H6 1 F
28 1 H_F2_6____28___ 2 F
Helpfully, this acts as a lookup table, with the atom label from the
res file and the DMACRYS label.
dmarel.axis
Using DMAREL and Neighbours, this file looked like this:
MOLX 1
X LINE CAR1 CODA CAR2 CODA 2
Y PLANE CAR1 CODA CAR2 CODA 2 OXY1 CODA 2
ENDS
But to use with DMACRYS and NEIGHCRYS, you should adjust it to use the
new atom labels, and drop the CODA keyword:
MOLX 1 X LINE C_F1_2____ C_F1_3____ 1 Y PLANE C_F1_2____ C_F1_3____ 1 C_F1_1____ 1 ENDS
Notice that is uses the short atom labels.
Also, the potential type must be correct.
Fort.21
With this axis file, you can now generate your molecular conformation
for Gaussian. Run NEIGHCRYS, with the files as before and your new dmarel.axis
file. Now, in fort.21 you will find the following familiar section:
Local axes from input dataset
Local axis set for molecule:
1
x=> -0.891615 -0.347799 -0.289928
y=> 0.199207 -0.876318 0.438615
z=> -0.406619 0.333320 0.850622
Atom positions in local axis
system for molecule 1
basis No. Species x y z (Angstroms)
Mass
1 C_F1_1____ -1.457148 -1.138491
-0.000054 12.010700
9 C_F1_2____ -0.776877 0.017477 -0.000054 12.010700
17 C_F1_3____ 0.695207 0.017477 -0.000054 12.010700
25 O_F1_1____ 1.380979 1.034138 0.000194 15.999400
33 H_F1_1____ -0.936056 -2.087754 -0.001291 1.007940
41 H_F1_2____ -2.536577 -1.170809 -0.000373 1.007940
49 H_F1_3____ -1.270829 0.980410 0.001203 1.007940
57 H_F1_4____ 1.159371 -0.987246 -0.000686 1.007940
basis No. Species x y z (AU)
Mass
1 C_F1_1____ -2.753612 -2.151436
-0.000102 12.010700
9 C_F1_2____ -1.468086 0.033026 -0.000102 12.010700
17 C_F1_3____ 1.313752 0.033026 -0.000102 12.010700
25 O_F1_1____ 2.609672 1.954238 0.000367 15.999400
33 H_F1_1____ -1.768890 -3.945285 -0.002440 1.007940
41 H_F1_2____ -4.793437 -2.212509 -0.000705 1.007940
49 H_F1_3____ -2.401519 1.852707 0.002274 1.007940
57 H_F1_4____ 2.190895 -1.865626 -0.001297 1.007940
This can then be used by GAUSSIAN to generate the wavefunction, for use
by NEIGHCRYS.
3. The new Williams Potential
We have all heard of the "Williams" potential as an update
to our present "FIT" potential. Presently our atom-atom potentials
define types based on atomic number (i.e CAR, NIT, OXY), with only one
set of parameters per type. The exception to this is hydrogen, which has
different parameters if it is bonded to oxygen, or nitrogen.
The Williams potential expands on this, with parameters for different
bonding scenarios, i.e. 2-, 3- and 4-coordinated carbon atoms; NH2+,
-NH, NC3 and N=N nitrogen, etc. This makes a lot of chemical
sense, and should improve our predictions. However there is one more factor
to the new potential, which also makes chemical sense: the parameters
are based on all bonds to hydrogen atoms being shortened by 0.1 Å.
Although the nuclear position may be well determined ab initio
or by neutron diffraction, the electrons, that is, the point at which
the forces act, are located between the hydrogen nucleus and the bonded
atom.
To cope with these new types there have been several changes to the now
familiar Neighbours and DMAREL codes. Usefully, but not most importantly
to the user, NEIGHCRYS will determine the atomic type and use the appropriate
atom-atom potential. Also, if required, it will foreshorten the hydrogen
bond lengths by 0.1 Å.
Now, you may be thinking that there is at least one problem caused by
this, and you would be correct. Firstly, doesn’t the centre of mass
change if you adjust the position of the hydrogen atoms? And aren’t
the atomic positions relative to the centre of mass? How can this be right?
Well, this is true, and it has an important implication for our work.
An ab initio package, like GAUSSIAN [Gaussian 03, Frisch et al,
Gaissian Inc.], needs to know the position of the nuclei because it will
deal with the electrons itself. But, and very importantly, we always use
NEIGHCRYS with our defined axis system to give us the atomic coordinates
relative to the centre of mass, so that our input structure from the SHELX
res file, our axes and our multipole moments are all consistent. Thankfully,
NEIGHCRYS knows what we need, and the coordinates of the atomic nuclei
are given correctly relative to the adjusted centre of mass.
4. How to do a proper run using the WILLIAMS
potential
This requires some modified versions of the programs you know. All of
the programs you need for this Williams run are supplied in the download
you will have received.
Below are the steps for minimizing a single crystal structure.
- Gather your SHELX file, your new bondlengths file, and your Williams
potential file (will01.pots)
- Run NEIGHCRYS and answer the questions as normal, with the files
that you have. NB: There are two new questions.
You DO want to use the Williams potential, and you DO
want to use foreshortened hydrogen positions.
- Create your dmarel.axis file using the atom labels in fort.21
- Run NEIGHCRYS with your new axis file
- Check that all your atoms are correctly typed in fort.21. Copy the
coordinates for molecule 1 in Å only, as you normally would, and
put them in your geom file. Do not be phased by the extra section for
hydrogens.
Local axis set for molecule: 1
x=> 0.356964 0.654013 0.666966
y=> 0.448954 -0.746252 0.491476
z=> 0.819156 0.123998 -0.560007
Hydrogen positions have been foreshortened.
Positions of all atoms (with hydrogens not foreshortened)
in the local axis system and centre of mass of the molecule
with foreshortened hydrogens for molecule 1
basis No. Species x y z (Angstroms) Mass
1 C_W3_1____ -0.766275 -0.000279 0.000774 12.010700
3 C_W3_2____ 0.766774 -0.000279 0.000774 12.010700
5 O_W1_1____ -1.433231 1.040756 -0.005307 15.999400
7 O_W1_2____ 1.433269 -1.041596 0.000774 15.999400
9 N_W3_1____ -2.619735 -1.511298 0.112844 14.006740
11 N_W3_2____ -1.231180 -1.259466 0.106814 14.006740
13 N_W3_3____ 1.231738 1.259770 -0.095336 14.006740
15 N_W3_4____ 2.619737 1.511681 -0.119590 14.006740
17 H_W4_1____ -2.743490 -2.486029 -0.134621 1.007940
19 H_W4_2____ -2.944737 -1.408808 1.070991 1.007940
21 H_W4_3____ -0.550925 -2.005695 0.052412 1.007940
23 H_W4_4____ 0.548220 2.003881 -0.052643 1.007940
25 H_W4_5____ 2.928963 1.423745 -1.084509 1.007940
27 H_W4_6____ 2.746009 2.484353 0.134988 1.007940
basis No. Species x y z (AU) Mass
1 C_W3_1____ -1.448050 -0.000528 0.001463 12.010700
3 C_W3_2____ 1.448993 -0.000528 0.001463 12.010700
5 O_W1_1____ -2.708415 1.966745 -0.010029 15.999400
7 O_W1_2____ 2.708487 -1.968333 0.001463 15.999400
9 N_W3_1____ -4.950583 -2.855940 0.213244 14.006740
11 N_W3_2____ -2.326594 -2.380046 0.201850 14.006740
13 N_W3_3____ 2.327649 2.380621 -0.180159 14.006740
15 N_W3_4____ 4.950586 2.856664 -0.225992 14.006740
17 H_W4_1____ -5.184447 -4.697915 -0.254397 1.007940
19 H_W4_2____ -5.564748 -2.662263 2.023881 1.007940
21 H_W4_3____ -1.041098 -3.790215 0.099044 1.007940
23 H_W4_4____ 1.035986 3.786787 -0.099481 1.007940
25 H_W4_5____ 5.534941 2.690489 -2.049426 1.007940
27 H_W4_6____ 5.189208 4.694749 0.255091 1.007940
foreshortened hydrogen atom positions in the same
local axis system
basis No. Species x y z (Angstroms) Mass
17 H_W4_1____ -2.731276 -2.389829 -0.110198 1.007940
19 H_W4_2____ -2.912778 -1.418886 0.976773 1.007940
21 H_W4_3____ -0.618196 -1.931900 0.057792 1.007940
23 H_W4_4____ 0.615808 1.930301 -0.056865 1.007940
25 H_W4_5____ 2.898560 1.432391 -0.989636 1.007940
27 H_W4_6____ 2.733548 2.388366 0.109865 1.007940
basis No. Species x y z (AU) Mass
17 H_W4_1____ -5.161366 -4.516125 -0.208244 1.007940
19 H_W4_2____ -5.504355 -2.681308 1.845834 1.007940
21 H_W4_3____ -1.168221 -3.650763 0.109211 1.007940
23 H_W4_4____ 1.163709 3.647741 -0.107458 1.007940
25 H_W4_5____ 5.477486 2.706827 -1.870143 1.007940
27 H_W4_6____ 5.165659 4.513359 0.207615 1.007940>
- Notice that I have used this time the Williams potential. These
example labels differ from those in the previous section, allowing you
to see the different types of labels. Obviously, if there were
no foreshortening of the bonds, then the last two sections would be
omitted. Please read the text in this example and realise what these
coordinates are. You may have realised that the top block of atomic
positions is what must be copied and placed in your mol.geom file, and
used for Gaussian. The lower block shows the hydrogen nuclei at their
foreshortened position, as used by DMACRYS with the Williams potential.
- Use these same atomic positions to generate your .com file for Gaussian,
and run the job
- You need a simple GDMA input file as before. You may use the same
input file as you have used before. However, you must use not gdma but
gdma_for. This will calculate the multipoles at the shortened hydrogen
positions, using GDMA2.2 (available
from Prof. Anthony Stone's group).
- At this point you would usually make a cadpac.charges file using
gdmaneigh. Instead, use gdmaneighcrys (supplied with your download).
Your answers will be as usual. This code will test the atomic coordinates
of all atoms between your geom file and your DMA file. They must be
the same (they should be unless you have made an error), but it allows
the hydrogen positions to be exactly 0.1 Å shorter.
- Now you have everything you need. Run NEIGHCRYS again, remembering
to answer that you are using the Williams potential with foreshortening
of bonds to hydrogen atoms. This will give you’re your usual dmain
file.
5. How to do a ‘wrong’ Williams run
You may have realised that it is possible to use the Williams potential
without foreshortening the hydrogen positions. This
is an incorrect use of the Williams potential. It should be clear
how to do this. Please don’t, unless you have a good reason.
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