Mr. Raval,

You do not need server (free online), if you use MD. You can download some of the free of charge packages (https://en.wikipedia.org/wiki/Category:Molecular_dynamics_software) and to run computations in your personal computer. Depending on the theoretical level and thepower of your machine you can compute about 20 000 atoms (even more) in a single run.

Then these systems/properties, which you have found as most important ones to your study you can compute at an increased accuracy in the server of your Institution.

In particular, only ligands you can run in your personal computer even at a high accuracy using ab initio methods.

Dear colleagues,

you can use:

AutoDock

Dock (Linux only)

I Gem Dock

ArgusLab

NRGsuite

Best regards,

Drago

Dear Mukesh,

Unfortunately, there is NO online server that a person can use. Generally, you have or your university has to purchase such one. The prices for such servers dependent on the memory of the server. However, as Drago mentioned in his answer, you can download one of the listed programs and run your calculations with.

Hoping this will be helpful,

Rafik

Dear Sir,

You can carry out with Schrodingers Desmond free software for molecular dynamics

Mr. Raval,

You do not need server (free online), if you use MD. You can download some of the free of charge packages (https://en.wikipedia.org/wiki/Category:Molecular_dynamics_software) and to run computations in your personal computer. Depending on the theoretical level and thepower of your machine you can compute about 20 000 atoms (even more) in a single run.

Then these systems/properties, which you have found as most important ones to your study you can compute at an increased accuracy in the server of your Institution.

In particular, only ligands you can run in your personal computer even at a high accuracy using ab initio methods.

Come one, people, docking is not the same as molecular dynamics. 

Actually, there IS an online tool, GROMACS web server:  http://www.wenmr.eu/wenmr/md-simulations-using-gromacs-web-server

But it has some limitations 

Hi Mukesh,

(Sorry, in my previous post, I must have overlooked the important keyword "molecular dynamics" via my mobile phone while on travel. Having a second look at this page on my desktop did I realize that I have not answered your question. Here is my second attempt.)

So you would like to perform MD online, in addition to the GROMACS web server suggested by Natalia, I would also recommend the following free server (requires registration):

1) MDWeb (see Link 1). This server supports MD of protein-ligand complex. Tutorial on using MDWeb is also provided on the website (see Link 2).

2) HADDOCK (see Link 3). HADDOCK is also hosted on the same server as GROMACS webserver mentioned above on the WeNMR infrastructure. HADDOCK supports a wide range of docking possibilities: protein-protein, protein-nucleic acids and protein-ligand complexes. An overview of the HADDOCK server is provided in a recent article published in Journal of Molecular Biology (see Link 4). Tutorial is also available on their website (see Link 5), on YouTube (see Links 6 and 7). A Nature Protocols on how to use HADDOCK is also available (Link 8).

Hope this helps.

Best regards,

Chanin

http://mmb.irbbarcelona.org/MDWeb

http://mmb.irbbarcelona.org/MDWeb/help.php?id=base

http://haddock.science.uu.nl/services/HADDOCK2.2/haddock.php

http://dx.doi.org/10.1016/j.jmb.2015.09.014

http://www.wenmr.eu/wenmr/haddock-web-server-tutorial

http://www.youtube.com/watch?v=5eS8BAOJ6es

http://www.youtube.com/watch?v=InwxoiVy3QQ

http://dx.doi.org/10.1038/nprot.2010.32

GROMACS, Desmond, NAMD-VMD are some of the popular freely available softwares for carrying out molecular dynamic simulations

Additional data from a more recent discussion in the same topic:

https://www.researchgate.net/post/Is_there_any_free_online_server_where_i_can_do_simulation_of_pdb_file_of_protein_for_more_than_10_ns?_tpcectx=profile_answers

Dear Prof. Bojidarka Ivanova,

In your comment you have mentioned that "Depending on the theoretical level and the power of your machine you can compute about 20 000 atoms (even more) in a single run". Could you please recommend some ab initio MD and DFT codes which can handle such a large number of atoms on a simple laptop (core i5 or i7)?

Thank you.

Ali