[gmx-users] Adding polarizability

Eric Shamay eric.shamay at gmail.com
Tue Nov 20 03:13:48 CET 2007

Dear gromacs community,

I've been trying to switch over from AMBER and I'm running into a few issues
that the manual doesn't clarify well enough for me. Can anyone point me to
information on adding in polarizability to atoms? In amber it was a simple
matter of adjusting the frcmod file, but I can't find the location to add
that info in for gromacs. Additionally, what do I need to do in terms of the
run-parameters and topology/force-field to enable polarizability (the
equivalent in AMBER would be IPOL=1)?

Secondly, if I'm looking to use the flexible SPC water (a la Ferguson) I've
found that I can specify the '-water spc' option during the pdb2gmx
conversion while choosing the gromacs 53a6 force field (not sure that it
makes a difference), and I add in the -DFLEX_SPC keyword under the 'define'
section of the grompp.mdp run-parameter file. Is that all I need to do, or
is there a missing or incorrectly done step before I can actually use the
flexible SPC?

Lastly, I would also like to use the anharmonic (cubic) term for the OH
stretching as per ferguson. What do I need to do to enable this?

Thank you,
~Eric Shamay
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