[Chimera-users] Molecular Dynamics

[Jean-Didier Pierre Marechal]

Dear Edmund,

Elaine is completely right about everything. This interface was first developed for our lab for our own needs (training, short MD and Teaching) then we work with the Chimera’s team to make it look the way it looks today (a lot better than the initial shot). 

It can do a lot of things but in its actual state it remains a simple tool for first insights on the system and not necessarily convenient for all systems (especially if you look for large systems with long MDs). Typical time scale of MDs in today standards are difficult to performe with this interface. The main application we make of it is on small molecules and for teaching purposes it is fantastic. You could eventually look look for short MDs on a complex protein-ligand but I would reckon to go for standard MD drivers. 

We did not continue on this project because ChimeraX, that already integrates openMM, was about to be relased.

Hope this help, 

JeanDI

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Prof. Dr. Jean-Didier Maréchal (JeanDi)
Associate Professor

Insilichem
Departament de Química
Universitat Autònoma de Barcelona
Edifici C.n.
08193 Cerdanyola (Barcelona)
Tel: +34.935814936
e-mail: JeanDidier.Marechal at uab.es
personal webpage: http://gent.uab.cat/jdidier
insilichem webpage: http://www.insilichem.com