[Chimera-users] Regarding MD simulation

[Francois Berenger]

On 11/06/2019 01:04, Elaine Meng wrote:
> Sorry, I do not have anything to say other than what is already
> written in the Molecular Dynamics Simulation manual page.
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>

Also, you might be interested by this article and the corresponding 
software:

---
LiGRO: a graphical user interface for protein–ligand molecular dynamics
paper: https://doi.org/10.1007/s00894-017-3475-9
software: https://www.ufrgs.br/lasomfarmacia/ligro/
---

I have not tried it, but it looks useful for beginners.

> You have to decide on settings in each of the four sections (Prep
> Structure, Solvation, Constraints Etc., Run Parameters) which are
> described in detail on that page, and then click Run.
> 
> Compared to the large programs that focus mostly on simulations, the
> MD tool in Chimera has only limited options, limited control over
> parameters, and is not very fast.  If you are going to do a research
> project that relies heavily on simulations, you may need to use one of
> those other programs instead (e.g. AMBER, GROMACS, …).  They are much
> more complex and probably take more time to learn, but they also have
> several tutorials and examples.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Jun 8, 2019, at 12:47 AM, Divakar S <divakar.s at jssuni.edu.in> 
>> wrote:
>> 
>> Hi,
>> I have been trying to do MD simulation in chimera. However, i could 
>> not understand the exact procedure from the user help menu. Plz give 
>> us a detailed procedure for simulation and analysis if possible. I 
>> also tried to learn the procedures from previously published papers 
>> but i couldn't find any articles using MD simulation from chimera.
>> 
>> Thank you
> 
> 
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