You want to set scmask to the empty string for one end state. If you
want to separate electrostatics from vdW transformation you can use
crgmask and run two simulations. You create two topology files: one
with Ni2+ and the second one without the Ni2+ (just remove the ion from
the coordinates). There should be no need for any TI/FEP specific
setup in leap.
Example mdin files:
vdW transformation:
1a)
ifsc = 1
scmask = ''
crgmask = '.Ni' ! set charges to zero
1b)
ifsc = 1
scmask = '.Ni' ! switch on the vdW interactions
crgmask = '.Ni' ! set charges to zero
electrostatic transformation.
2a)
ifsc = 0
crgmask = '.Ni'
2b)
ifsc = 0
Cheers,
Hannes.
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Received on Mon Apr 17 2017 - 03:30:02 PDT
