[gmx-users] Polarisable water topology / Ions
maxim.fedorov at ucd.ie
Fri Mar 10 20:56:49 CET 2006
1. Does anybody have a 'ready-to-run' topology
for SW water (the polarisable water model from J.Phys. Chem. B (2001),
As I see the sw.itp in the standart distribution
has improper order of directives. Am I right or it is just the Friday
night and I should take a rest for a while...?
the grompp also tells me: "Invalid order for directive defaults, file
""/home/users/mfedorov/utils/gromacs/share/gromacs/top/sw.itp"", line 35
I am able to prepare this topology by myself but it would cost me some
time. And I can also make a mistake - I am a human being at the end ...
Is there a good soul which help me to save this bit of my life-time? If
somebody has a box of the sw - water I'll tell him many-many thanks as well.
2. Can anybody give me a piece of advice about ion parameters which work
more or less well for SW? I would appreciate
any link for literature or just parameters.
Many thanks to all who participated in the discussion about the
influence of Counterions on protein Dynamics.
I can see now that the effect of Poly-L-Lysine unfolding is quite
sensitive to FF parameters, water model and E-treatment.
The simplest solution was to add more co-ions which broke
that 'trap'. Anyway I am looking for a suitable water model for this
effect, that's why I would like to try SW.
All the best,
Maxim V. Fedorov
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