[gmx-users] reference for make_edi -linacc

chris.neale at utoronto.ca chris.neale at utoronto.ca
Fri Dec 18 16:48:06 CET 2009


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  

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,

More information about the gromacs.org_gmx-users mailing list