GROMACS binaries are available for Macs http://www.gromacs.org/content/view/32/100/
Afaic, GROMACS is user-friendly. There are good tutorials, and there is even third-party GUI: http://resal.atspace.com/grogui.htm IMHO, the GUI is not much better than running Gromacs jobs from command line, but it is rather helpful with visualization of energy trends, etc. HTH. On Thu, 2008-07-03 at 12:20 +0100, Martyn Winn wrote: > Gromacs www.gromacs.org > > It is GPL. It can certainly handle metals, although as is always the > case, you have to be careful in the choice of force field. It is fairly > user friendly (by the standards of that field ;-). Not sure what the > situation is for Macs but certainly runs well on Linux. > > Alternatives: charmm, amber, namd, etc etc > > Your suggested project is perfectly reasonable, but don't expect it to > be a day's work .... > > HTH > Martyn > > > On Thu, 2008-07-03 at 11:30 +0100, David Briggs wrote: > > Hi everyone. > > > > I have a slightly off topic question I hope someone can help with. > > > > I have a structure of a wild type domain, which binds metal ions. > > Certain mutations in chelating residues cause changes in the apparent > > affinity for said metal ions. > > > > As I have (so far) failed to crystallise the mutant, I would like to > > do some molecular dynamics in a water box, (with afore mentioned > > mutations) to get a handle on the origin of the change in metal ion > > affinity. > > > > Does anyone know of a suitable package which: > > > > a) is open source, or basically free to academics > > b) allows inclusion of metal ions > > c) gives an understandable and interpretable output, in terms of > > changes in energy, etc. > > d) Preferably runs on mac, (although I do have access to linux as well.) > > > > Am I asking for the moon on a stick? > > > > Looking forward to your responses. > > > > Regards, > > > > Dave -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse /
