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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