Dear friends and fellow researchers,
Currently I am working with some chemozenzitizing agents and I am planing to extend it by performing molecular dynamic simulations with selective proteins. Could anyone help me by proving a protocol for gromacs (in UBUNTU LINUX) and could you please provide me with any GUI for Gromacs.
The biggest challenge is not running MD, rather it is the parametrization of whatever your chemosensitizing agents are. These will be non-standard species and will require great care to derive suitable parameters. The protein component and the overall simulation protocol are straightforward.
Hi Deepak,
You should check the below link.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/
Well I prefer command line over GUI. If you want you can edit those scripts mentioned in the tutorials to get better results.
I will highly recommend to follow GROMACS mailing list. You might get quick responses there.
Cheers!!
The biggest challenge is not running MD, rather it is the parametrization of whatever your chemosensitizing agents are. These will be non-standard species and will require great care to derive suitable parameters. The protein component and the overall simulation protocol are straightforward.
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