modified on 5 October 2011 at 13:07 ••• 11,975 views

Qmmm preparation solvation

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QM/MM Restart and Topology files: Prerequisites | QM region definition | Solvation | Permanent Constraints

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
source etl0.pdb
new_top new_seq
#center and orient prior to solvation
#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
write etl_ref.rst
write etl_ref.pdb
task prepare