[gmx-users] (no subject)

Covington, Cody Lance cody.l.covington at Vanderbilt.Edu
Mon Jul 23 22:28:02 CEST 2012

Dear gmx-users

I am trying to calculate the optical rotation of a molecule in solution. There are several examples of this in the literature where they take snapshots of molecule at intervals throughout the trajectory, calculate optical rotation, and average them to get a solvated optical rotation. I have tried using this method by my numbers don't seem to converge on any one value, for example over 6ns trajectory, using 3000 snapshots I get a calculated rotatory power of ~20 deg/cm average with a standard deviation 745 deg/cm! (calculated with atom-dipole interaction model). my molecule does have a long carbon chain which may be the problem.
So would it help to pick out the most common configurations and do calculations on them perhaps?
is there a feature of gromacs that will determine the most probable conformations? 
Also I set up an single point energy calculation of each snapshot using  mdrun -rerun  (but this is on the unsolvated molecule) for possible comparison of the snapshot energies, but is there a better way of getting these energies from the energy file?

Thanks in advance for any responses
Cody Covington 

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