[gmx-users] Questions about implementing G56A_CARB parameters

Jon Kapla jon.kapla at mmk.su.se
Sat Mar 12 13:09:14 CET 2011


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/. 
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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