parichita parichita wrote:
Thaks for your suggesion...
I want to use Gromacs for MD on my disaccharides in explicit water box.Now, the
problem I encounter is that the pdb2gmx produces the topologies where hydrogens
sitting on carbons are condensed on carbon atoms they sit on. I need them explicitly
since I would like to study the NMR coupling contanst of hydroxy protons and C-H protons.I
mean 3J(H-O-C-H) and measure the distance between the C-H proton through the glycosidic linkage.
So my questions are;
1- Are the force fields(45a3,53a5) that are implemented in Gromacs capable of taking care
of hydrogens sitting on carbon atoms in a sugar molecule explicitly?
See below, and http://wiki.gromacs.org/index.php/Force_Fields
2- How can I most reliably produce topologies for my disaccharide that will
be placed in a water box to perform MD?
pdb2gmx... you should find and do some tutorial material to learn about
this.
I am quite new to MD methods therefore I apologize already now if I put
forward something incoherent.
You should definitely be doing some background reading of textbooks and
tutorials if you haven't yet come across the phenomena of united-atom
and all-atom force fields. MD simulations are fabulously easy ways to
generate very expensive random numbers, and there's no substitute for
library work and careful experimentation. The first few chapters of the
GROMACS manual are a good place to start.
Mark
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