Qmmm preparation solvation
During the preparation stage of QM/MM calculations the system may also be solvated using solvate directive of the prepare module. It is recommended that solvation is performed in conjunction with center and orient directives.
Here is an example where the ethanol molecule is declared quantum and solvated in a box of spce waters:
title "Prepare QM/MM calculation of solvated ethanol" start etl prepare source etl0.pdb new_top new_seq new_rst #center and orient prior to solvation center orient #solvation in 1 nm by 2 nm by 3 nm box solvate box 1.0 2.0 3.0 #the whole ethanol is declared quantum now modify segment 1 quantum update lists ignore write etl_ref.rst write etl_ref.pdb end task prepare