MM and QMMM example inputs

Ewald Pauwels ewald.... at ugent.be
Mon Jan 26 12:27:52 CET 2009


Dear all,

Quite a while ago, I kinda promised to try and make some example input
files for MM and QM/MM calculations. They are finished now and I
uploaded them as 'Charmm_qmmm.tar.gz'.

I made an example tripeptide (trialanine), which was solvated in
water. The forcefield is CHARMM.
The tar-file contains the necessary psf/pdb files and three
inputfiles:
- MinMM: an example geometry optimization using FIST (only MM)
- MinQMMM: now using the QMMM routine with mechanical embedding; the
entire protein is in the QM layer
- MinQMMM_link: GEEP for the electrostatic coupling between QM and MM;
only the central Ala residue is in the QM layer; two link atoms were
introduced

Some technical remarks:
1/ Charmm parameters and topology files were downloaded from the
Mackerell-site (google).
2/ Regarding pdb/psf files
* created using vmd, the manual and tutorials should be sufficient to
create these files
* removed "CMAP" in the header of the psf file
* the box size and amount of water is quite (too) small
3/ Regarding Minimization
* The initial geometry is far from perfect. To avoid errors at the
beginning of the optimization, the NEIGHBOR_LISTS/GEO_CHECK setting is
(initially) set to false.

I would really appreciate it if people could check whether there are
still errors in the input.
If more information is desirable, feel free to mail me.

Sincerely,
Ewald.


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