[gmx-users] reference for make_edi -linacc

Carsten Kutzner ckutzne at gwdg.de
Fri Dec 18 17:41:08 CET 2009

Hi Chris, 

I think linacc never rejects steps (the make_edi help is not quite correct here I am 
afraid) but either accepts them if they go into the right direction or otherwise 
corrects them. This way the system will without stalling go into the desired 
direction with respect to the selected eigenvector. From a quick look on the
paper I assume that they are using the radacc method there.


On Dec 18, 2009, at 4:48 PM, 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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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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