[gmx-users] reference for make_edi -linacc

chris.neale at utoronto.ca chris.neale at utoronto.ca
Fri Dec 18 17:04:50 CET 2009

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,

-- original message --

Hi Chris,

Maybe in this paper:

Daidone et al., Molecular Dynamics Simulation of Protein Folding by
Essential Dynamics Sampling: Folding Landscape of Horse Heart Cytochrome c


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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