On 4/07/2012 11:43 PM, Michael Brunsteiner wrote:
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
Recent versions of spc.itp files include a flexible (ie. non-settle)
version that you could be using easily with -DFLEXIBLE.... see
http://www.gromacs.org/Documentation/Include_File_Mechanism.
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)
h-angles converts bonds to constraints, but there have to be [bonds].
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?
As you are doing, but better :-) -DFLEXIBLE and h-angles should work well.
Mark
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