[gmx-users] LIE interaction energy calculations

Anton Feenstra feenstra at chem.vu.nl
Wed May 14 09:52:02 CEST 2003

Hi All,

I'm in the middle of performing LIE calculations, or rather LIE analysis
of my simulations. The problem I have is that traditionally, LIE is
performed on/with short simulations of ~100ps, with a substrate in a
more or less confined binding pocked. Optionally, results from several
simulations in different binding modes (orientations) can be combined.

I am facing substrates without confined binding, i.e. they have much
room to move around in the active site and binding region, but do stick
preferentially to some (several) locations. In that light, I did several
very long (>5 x 10ns) simulations to get the best possible sampling.

My problem now is how best to combine these results. For the short
simulations of more or less well-defined binding modes, the energies are
averaged per simulation, and then averaged with their respective Boltzmann
weights, so that high energy (and thus less likely) states weigh less.
Doing that for my long simulations produces nonsense results, so I was
thinking of taking already the boltzmann-weighing for the average over
the simulations. The problem I have with that, is that there is of course
already a Boltzmann factor involved due to the statistical sampling
during the simulation, so it would seem that I boltzmann-weigh it twice.

Has any of you thought about this and come up with some ideas or
suggestions...? Any input is much appreciated!


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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