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.ne...@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. > > --gmx-users mailing list gmx-users@gromacs.org > 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 thewww > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
