[Chimera-users] Molecular dynamics simulation plugin

[Enrico Martinez]

Dear Chimera Users,
I have a question related to the molecular dynamics simulation plugin
integrated into the Chimera. As I understand it correctly, Chimera
uses Amber integrated into the GUI.  Here are my questions:

1) What are the limitations of this version of MD engine compared to
the Amber software, which we may use to run molecular dynamics in
terminal?

2)May I increase the integration step to 2 fs (assuming that there are
constraints on the hydrogen atoms) during the production phase?

3) how the ligands may be parametrized ? What is the difference
between two methods that are used for charges ?

4) Is it really slower compared to Amber ? May I use multi-cpu
stations for the run ? I've just made it on my iMAC with 6 available
CPUs but would like to try on the 96 CPUs linux station.
Yours with thanks
Enrico