[gmx-users] Dihedral time of circulation

[chris . neale]

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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[gmx-users] Dihedral time of circulation

[chris . neale]

100 fs = 50 timesteps? I doubt it, but then again I have never checked  
and you're talking about a chi3 here, and one that involves a S with  
no hydrogens at that so I guess that it could occur quicker than I  
expected. However, you should avoid talking about time for one  
rotation without error bounds here as it's also possible that you are  
seeing some non-equilibrium equilibration to relieve bad contacts in  
your initial structure.


-- original message --

Dear all,

perhaps I have to be more clear:

I made I short MD with OPLSAA/tip4p and PME of Gly-Met-Gly. If I plot  
the CB-CG-SD-CE dihedral on the time scale I get the shortest time for  
a whole rotation of about 100 fs. So, my question is, if this value is  
reasonable or not?


I suppose there must be some experimental data or should I expect this  
time scale.


Sasa



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