[gmx-users] water with atom-based cut-off ...

[Michael Brunsteiner]

hi,

i'd like to do a simulation of a solute in water - trying to reproduce some literature data
i try to be consistent and use an atom-based cut-off. for this each atom needs to be
its own charge-group ...
so when i change spc.itp
from:
     1  opls_116   1    SOL     OW      1      -0.82
     2  opls_117   1    SOL    HW1      1       0.41
     3  opls_117   1    SOL    HW2      1       0.41
to:
    1  opls_116   1    SOL     OW      1      -0.82
    2  opls_117   1    SOL    HW1      2       0.41
    3  opls_117   1    SOL    HW2      3       0.41

grompp complains that for settle all atoms need to be in the same charge group.
so i removed the settle and exclusion statements from spc.itp and instead
put the commands


constraints               = h-angles
constraint_algorithm  = LINCS
lincs_order                = 8
lincs_iter                   = 2


in the mdp file ... but now constraints are not applied to waters at all (O and H look as if they move independently)
it also didn't help renaming the water molecule, residue and atom names ...

any suggestions on how i can apply atom-based cut-off with lincs or shake to water?

thanks,

michael


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