[Chimera-users] Molecular dynamics simulation plugin

[Elaine Meng]

Hello,
The documentation explains that this MD simulation tool uses MMTK to run the dynamics, not AMBER.  Only the force field parameters are from AMBER.  

This MD tool was implemented by another lab (Victor Muñoz Robles and Jean-Didier Marécha, Universitat Autònoma de Barcelona) in collaboration with ours, so I cannot say more than is already in the documentation, so please see:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>

(1) as comparedthere are many fewer options and thus less control over settings (e.g. no nonbonded cutoff, no way to add individual restraints, probably dozens of other things)

(2) yes as you can see in the dialog, time step is a user-adjustable option for both equilibration and production dynamics

(3) this is all described in the Minimize Structure and Add Charge documentation, see the following and links therein:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html>
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#parameters>

(4) of course it depends on all the settings in the two programs, but in general yes, much much slower than AMBER

Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 21, 2022, at 12:57 AM, Enrico Martinez via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> 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