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.
Carsten On Dec 18, 2009, at 4:48 PM, [email protected] 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. > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
