[gmx-users] reference for make_edi -linacc

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

Re: [gmx-users] reference for make_edi -linacc

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

[gmx-users] reference for make_edi -linacc

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, Chris. -- original message -- Hi Chris, Maybe

Re: [gmx-users] reference for make_edi -linacc

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