[gmx-users] Adding polarizability

David van der Spoel spoel at xray.bmc.uu.se
Tue Nov 20 08:13:33 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)?
As Mark answered there is no out of thebox polarizability. AFAIK there 
is no complete force field like that in Amber either, only Tinker has one.
> 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?

there is flexspc.itp with this model. There is also TIP4P/Flex.

> Thank you,
> -- 
> ~Eric Shamay
> ------------------------------------------------------------------------
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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