Than you Ran, this looks good. The method is basically the same with
the exception that Daidone et al. utilize a target structure as
opposed to a target eigenvector, although the difference here is
probably semantic.
I greatly appreciate it,
Chris.
-- original message --
Hi Chris,
Maybe in this paper:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1303567/
Daidone et al., Molecular Dynamics Simulation of Protein Folding by
Essential Dynamics Sampling: Folding Landscape of Horse Heart Cytochrome c
Ran.
chris.neale at utoronto.ca wrote:
Hello,
does anybody have a reference for the -linacc method applied by
make_edi/mdrun? I have checked the references mentioned in make_edi -h
as well as the manual, but didn't find anything that matches -linacc
exactly.
For example, gromacs suggests that entire MD steps will be accepted or
rejected if they do or do not move in the desired direction along the
selected eigenvectors, respectively:
-linacc: perform acceptance linear expansion along selected eigenvectors.
(steps in the desired directions will be accepted, others will be
rejected).
While the published version appears to be more complex:
B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C.
Berendsen;
An extended sampling of the configurational space of HPr from E. coli
PROTEINS: Struct. Funct. Gen. 26: 314-322 (1996)
Briefly, the algorithm consists of the following steps: a starting
position is defined as the set of essential coordinates of the
starting conformation; a number of regular MD steps is preformed; for
each step, a new starting position is accepted only if it is not
closer to the starting position than the previous position, in the
subspace defined by the first three eigenvectors (i.e., if the
distance from the starting position in this subspace does not
decrease). If the new position is closet to the starting position, a
correctio is applied only in the subspace defied by the first three
eigenvectors with least perturbation.
Thank you,
Chris.
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