Molecular dynamics run

Dear CCL USers,

I have a huge protein Under study. I would like to subject it to MOlecular Dynamics. My forcefield limits me to take only 20 A of the protein from the active site. So i had to fix the protein 10A away from the active site and perform Molecular dynamics only for the active site. I continued MD with NVT ensemble.

Do the results i get are reliable. As i am fixing the protein to some extent do i need to compensate this constraint with some thing else.

Please let me know

Thanking you,


-Vema Aparna  Research Scholar
Prof. G.R. Desiraju's Group, School of Chemistry
University Of Hyderabad, Hyderabad - 500 046 INDIA

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