Is possible to simulate a trimer using gromacs package?

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Chanin Nantasenamat

Yes, it is possible to simulate a trimer. I've previously performed MD simulation of hemoglobin (a tetramer).

Nubia Toman

Dear Chanin, thanks for reply,

Can you give a tutorial, or some link to follow?

Vikash Kumar

Yup , it is possible to simulate trimer. Just use Pdb2gmx command . Gromacs will create a topology file containing the topology of all chains.

Simone Brogi

hi you can simulate all that you want by using GROMACS!!!

Justin Lemkul has an excellent tutorial on using GROMACS. The group of Prof. Bonvin also has got some great step-by-step tutorial.

Links are appended below.

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/

http://nmr.chem.uu.nl/~tsjerk/course/molmod/index.html#introduction