Hi I am looking for a MD simulation calculations for Small molecule-Protein interaction. But right now I am limited to Windows. So please let me know if there is any software which is useful in windows.
Dear Arvind,
If this is your first time running Molecular Dynamics simulation then I would highly recommend Yasara Structure (see link below) as it allows you to perform MD simulations as well as protein-ligand docking all on the Windows OS. The MD or docking calculations can be easily carried out using the provided Macro. Our experience using Yasara Structure in one of our previously published work on Aromatase-small molecule docking (see link below) which ran smoothly for 100 ns without a problem even after we shut the computer down it can be easily resumed. You can also see in real-time how the small molecule moves inside the protein cavity. Yasara Structure is also easy to understand and implement in your own work. The MD engine is based on YAMBER.
Hope this helps. Good luck in your endeavor!
http://www.yasara.org/products.htm
http://dx.doi.org/10.3390/molecules16053597
Most MD software (Gromacs, Desmond, NAMD...) work on windows. The more important question is hardware - do you have adequate RAM, cache, processor speed, hard disk space, cooling, ....? Multiprocessor and GPU systems enable quicker results.
yes dear you can use drug discovery studio 2.5 version aur which version u prefer , and also can use schrodinger mestro suit 9.1 on windows but i suggest you to gromacs and namd on linux for molecular dynamics simulation.
Hi, you can use NAMD.
http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName
Dear Arvind Negi,
Try to install the GROMACS package on Windows, following this procedure:
http://www.gromacs.org/Downloads/Installation_Instructions/Windows
Kind regards,
Arlan.
Dear Arvind,
If this is your first time running Molecular Dynamics simulation then I would highly recommend Yasara Structure (see link below) as it allows you to perform MD simulations as well as protein-ligand docking all on the Windows OS. The MD or docking calculations can be easily carried out using the provided Macro. Our experience using Yasara Structure in one of our previously published work on Aromatase-small molecule docking (see link below) which ran smoothly for 100 ns without a problem even after we shut the computer down it can be easily resumed. You can also see in real-time how the small molecule moves inside the protein cavity. Yasara Structure is also easy to understand and implement in your own work. The MD engine is based on YAMBER.
Hope this helps. Good luck in your endeavor!
http://www.yasara.org/products.htm
http://dx.doi.org/10.3390/molecules16053597
You can use LAMMPS, it has an exe file adapted with windows environment.
Thanks for everyone answers. @ Chanin Is it come with free academic licence.
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