About RMSD based PMF's

From: Felipe Merino (felmerino_at_uchile.cl)
Date: Thu May 13 2010 - 23:03:44 CDT


Maybe i am a little lost with this, but i have been performing some PMF
calculations using RMSD as the order parameter. As the simulations
approaches zero RMSD the free energy becomes very high i guess caused by
a "conformational stretching".
If we consider the number of microstates (really the volume of the phase
space compatible with the E + dE energies given by the hamiltonian -
including the harmonic RMSD constraint) that the system can show as a
function of RMSD they seem to have an inverse relation, Indeed it is
obvious when you consider that for the extreme case where RMSD is 0
there is just one microstate possible (considering only the constrained
atoms). This should put an extra entropic component in the reconstructed
PMF that i do not know if NAMD accounts for. I think that could explain
some crazy things that i see on my PMF's.

Any hints would be appreciated



Laboratorio de Bioquímica y Biología Molecular
Facultad de Ciencias
Universidad de Chile

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