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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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