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Hi,<br>
<br>
I'm about to simulate a disaccaride in water.<br>
Reading through the paper from Hansen and Hünenberger:<br>
<br>
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.<br>
Hansen, H. S.; Hünenberger, P. H. <i>Journal of computational
chemistry</i>. 2010.<br>
doi: 10.1002/jcc.21675<br>
<br>
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.<br>
<br>
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.<br>
<br>
The torsion angle function given in the gromacs manual is exactly
the same as they give in the paper above.<br>
<br>
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.<br>
<br>
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?<br>
<br>
Best regards<br>
Jon Kapla<br>
<br>
<br>
<br>
<br>
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