Hi all,
we've been performing some PMF calculations related to the change of a
dihedral angle in a certain region of a protein. We've used the Ewald
sumations technique because it gave us very good results in our previous
MD simulations.
But unfortunately these PMF calculations have'nt succeed; the differences
in energy obtained don't correspond to the 'real' (experimental, in fact)
distribution of population of the rotational conformations. Performing the
same calculations without Ewald we get the 'correct' (experimental, again)
results.
Has anybody experienced something similar, and has any explanation for
this results? Does the Ewald method as implemented in AMBER 5.0 work for
PMF technique?
Thank you in advance.
Xavi
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_/ _/
_/ Xavier Deupi-Corral _/
_/ Computational Medicine Lab _/
_/ Biostatistics Unit. School of Medicine _/
_/ Universitat Autonoma de Barcelona _/
_/ CATALUNYA _/
_/ _/
_/ Phone : (3493)-581.23.48 _/
_/ E-mail : xavi_at_yogi.uab.es _/
_/ _/
_/ 'We are prisoners of our force field' _/
_/ _/
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Received on Thu Sep 23 1999 - 23:39:52 PDT
