[gmx-users] Adding polarizability

Mark Abraham Mark.Abraham at anu.edu.au
Tue Nov 20 04:41:38 CET 2007

Eric Shamay wrote:
> 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)?

GROMACS only does polarizability using shell functions (see various 
sections of the GROMACS manual), and there's no out-of-the-box AMBER 
equivalence implemented.

> 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?

Don't know. Please put different subjects in a different email, so that 
people can usefully use the email subject line to discard emails of no 
interest to them. This means you increase your chances that someone who 
knows your answer will read your email :-)

> 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?

Don't know. Chapters 4&5 of the manual treat such topics, if they can be 


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