Hi,
I'm about to simulate a disaccaride in water.
Reading through the paper from Hansen and Hünenberger:
A reoptimized GROMOS force field for hexopyranose-based carbohydrates
accounting for the relative free energies of ring conformers, anomers,
epimers, hydroxymethyl rotamers, and glycosidic linkage conformers.
?Hansen, H. S.; Hünenberger, P. H. /Journal of computational chemistry/.
2010.
doi: 10.1002/jcc.21675
it seems like a very rigid work and a good force field to use, since it
is directly based on the G53a6 ff already included in gromacs.
In the above paper they state that they introduce some things not
implemented according to the buildup rules and functionals of the
gromos96 program (but part of the upcoming version as of November 2010
though). These things are mainly the ability to use other torsional
phase shifts than 0 and 180 degrees and the addition of some 1-3
Lennard-Jones interactions for improved six ring stability.
The torsion angle function given in the gromacs manual is exactly the
same as they give in the paper above.
Thus, my first question is if gromacs have any restrictions on the
phase shifts, or if I directly can use the additional shifts of -60 and
60 degrees from 56A_CARB.
The second question is about the 1-3 interactions. What's the best way
of implementing this? Can I use an nrexcl of 2 and then add the wanted
interactions to the pair list and all other to the excluded
interactions? Do you have any other suggestions?
Best regards
Jon Kapla
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