An alternative repulsion-dispersion potential was parameterized to have the interaction sites of hydrogen atoms 0.1 Angstroms along the bond toward the heavier atom. The reason for this is similar to the systematic shortening of bonds to hydrogen in X-ray structure determinations - as a hydrogen atom only has 1 electron, the effect of the electron is not evenly distributed around the nucleus as for other atoms but closer to the centre of the bond. This potential requires the use of foreshortened hydrogen atom positions. If you answer the questions in NEIGHCRYS stating that you want to use the Williams potential and foreshorten bonds to hydrogen, you will get a section similar to the following in your fort.21 file (this is taken from example 02 in the test suite).
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 0.850622Hydrogen 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____ -1.458147 -1.140153 0.000056 12.010700
9 C_W3_2____ -0.777876 0.015814 0.000056 12.010700
17 C_W3_3____ 0.694209 0.015814 0.000056 12.010700
25 O_W1_1____ 1.379980 1.032476 -0.000193 15.999400
33 H_W1_1____ -0.937054 -2.089416 0.001293 1.007940
41 H_W1_2____ -2.537575 -1.172471 0.000375 1.007940
49 H_W1_3____ -1.271827 0.978748 -0.001202 1.007940
57 H_W1_4____ 1.158373 -0.988909 0.000688 1.007940basis No. Species x y z (AU) Mass
1 C_W3_1____ -2.755499 -2.154577 0.000105 12.010700
9 C_W3_2____ -1.469972 0.029885 0.000105 12.010700
17 C_W3_3____ 1.311865 0.029885 0.000105 12.010700
25 O_W1_1____ 2.607785 1.951097 -0.000364 15.999400
33 H_W1_1____ -1.770777 -3.948426 0.002443 1.007940
41 H_W1_2____ -4.795324 -2.215650 0.000708 1.007940
49 H_W1_3____ -2.403406 1.849566 -0.002271 1.007940
57 H_W1_4____ 2.189008 -1.868767 0.001300 1.007940Foreshortened hydrogen atom positions in the same
local axis systembasis No. Species x y z (Angstroms) Mass
33 H_W1_1____ -0.985175 -2.001756 0.001179 1.007940
41 H_W1_2____ -2.437620 -1.169478 0.000345 1.007940
49 H_W1_3____ -1.226185 0.889771 -0.001086 1.007940
57 H_W1_4____ 1.116434 -0.898128 0.000631 1.007940basis No. Species x y z (AU) Mass
33 H_W1_1____ -1.861712 -3.782771 0.002227 1.007940
41 H_W1_2____ -4.606436 -2.209995 0.000652 1.007940
49 H_W1_3____ -2.317156 1.681425 -0.002052 1.007940
57 H_W1_4____ 2.109755 -1.697216 0.001192 1.007940
In this case, you should take the first section with the Positions of all atoms (with hydrogens not foreshortened) (in Angstroms) forward to the GAUSSIAN charge density calculation.
Following this, you should NOT run gdma as normal. The programme gdma_for.f90 is included in the DMACRYS release. You must edit line 14 of this to point to your local copy of the gdma executable, and then compile it, and use this to run gdma. This will alter the distributed multipole analysis about the molecule, so that the interaction sites for hydrogen are 0.1 Angstroms along the bond, but the nuclear positions remain unchanged.
After this, run gdmaneighcrys as normal to get the dmacrys.dma file for your proper run of NEIGHCRYS and DMACRYS. gdmaneighcrys will check that the nuclear positions are the same in your mol.geom file and gdma.dma file (a very small tolerance is allowed), but it WILL NOT check that you have moved the interaction positions of your distributed multipole analysis.