Dear Sa?a:
There are many dihedral angles in the MET sidechain. I suspect that
you mean to ask "how long does it take the chi1 dihedral angle of MET
to equilibrate rotametric preference"?
The answer is entirely dependent on context, with a free amino acid
(perhaps also a methionine dipeptide) having the lowest correlation
time. This time, however, will always be very long on simulation
timescales.
Note also that the time required in simulation may or may not match an
experimental value if one exists.
If you want to get a lower bound for the time required, I suggest that
you put a methionine dipeptide (or free methionine if you must) in
vacuum and use the sd integrator. You should be able to get hundreds
of us per day on a system like this. Obviously the time that you
observe here will be significantly less than the time required in bulk
water, and the time required in a solvated protein context is likely
larger, and in the context of a protein embedded in a lipid bilayer
this will be even larger.
Still, this is a simple method to find out some number that represents
the absolute fastest that this could occur.
I do realize that the sd integrator time does not map directly to that
of the md integrator for kinetics (with a given tau_t), but this isn't
intended to be all that accurate, just to be something that you could
probably calculate in one day. If you need something more accurate
then it will take you longer. (You could use the md integrator in a
box of water with PME for example, but that will be much more
expensive -- putting a few METs in the same box might be useful here
if you position restrain a single backbone atom to ensure that they do
not contact each other).
Chris.
-- original message --
I have a question about dihedral time of circulation: what is the
typical time for a rotation of 360 deg of an unconstrained dihedral in
the side chain of an amino acid at 300K ? For example dihedral
rotation of MET side chain in a ALA-MET-ALA side chain. A use
OPLSAA/tip4p FF.
Many thanks
Sa?a
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