From: James Starlight (jmsstarlight_at_gmail.com)
Date: Sun Nov 03 2013 - 08:17:51 CST
Dear Namd users!
Recently I've decide to practice of accelerated MD insted of stered MD for
the increasing sampling of the conformational space of my protein.
Briefly this method is based on the addition of the boost potential to the
selected term of potential energy function (I'd like to use boost only
applied to the dihedral term yet) This setup consist of only 2 extra
parameters:
E threshold (boost aply only if the U < Eth to add some energy and force
system jump from the potential minimum ) as well as alpha- modulating
parameter which modulates the rooghness of new pot. surface ( the bigger
alpha the lowest bost so the new potential is closely to the initial one ).
In literature I found some empirical formulas for both bost and apha
implemented for the Amber 99 SB.
In case of dihedrals boost is dependent on the number of residues
Eth= U+1/3*number of atoms
alpha 4/5* number of atoms
Does some one use such technique in NAMD with both membrane and
water-soluble proteins (charm36 force field)? What parameters have
conclude to more biological-relevant transitions (in comparison to the
existing x-ray data for instance)? In what ensemble (nvt or npt) such aMD
could be performed ( I've seen implementation in nvt and not sure why I
cant use npt) ?
James
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