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 -- *Dr. Divakar S, M. Pharm (Pharmacology), PhD.,* *Lecturer, **Department of Pharmacology,* *JSS College of Pharmacy,* *(A Constitute College of JSS Academy of Higher Education and Research, Mysuru)* *Ooty, The Nilgris, Tamilnadu.* *Mobile: +91-9944036345* *Email: divakar.s@jssuni.edu.in <divakar.s@jssuni.edu.in>, diva.niru@gmail.com <diva.niru@gmail.com>*
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> 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@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
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@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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participants (3)
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Divakar S -
Elaine Meng -
Francois Berenger