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QM/MM Output: Simulated Annealing<br />
• Output files <br />
– QMMM_ORDER: <br />
– CRD_INI.g96 / CRD_FIN.g96 <br />
# Total number of atoms Number of QM atoms <br />
# NRTOT = 3544 NATq = 10<br />
#<br />
#__GROMOS_____CPMD_______is_______ia___SYMBOL_<br />
4 1 1 1 H<br />
5 2 1 2 H<br />
...<br />
GROMOS no. / CPMD no. / CP species no. / no. in the list <br />
of atoms for this <br />
(QM atoms come first) <br />
species <br />
• Ini4al and final coordinate files in GROMOS96 extended format. <br />
– interacting.pdb / interacting_new.pdb<br />
• Contains all QM and MM atoms in the electrosta4c coupling NN list (non-standard<br />
PDB format). <br />
ATOM 1 O QUA 2 3.501 5.134 5.831 0.00 10<br />
ATOM 2 C QUA 2 4.350 5.448 5.058 0.00 7<br />
ATOM 3 C QUA 2 5.419 4.483 4.605 0.00 8<br />
ATOM 4 H QUA 2 5.066 3.511 4.957 0.00 1<br />
...<br />
QM atom <br />
label <br />
GROMOS atom <br />
number <br />
CP atom number as <br />
in the trajectory file
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