modified on 11 September 2014 at 15:03 ••• 1,239 views

Release66:Qmmm preparation solvation

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Template:Release66:QMMM Restart and Topology Files Links


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