AMBER Archive (2009)

Subject: [AMBER] why is nonpolar solvation energy not implemented for dynamic in amber

From: TaoPaul (paultao2008_at_hotmail.com)
Date: Wed Aug 19 2009 - 10:29:38 CDT

Dear Amber developers

I am curious about that why nonpolar solvation energy is not implemented for dynamic PB calculation while it is implementd for static, as mentioned in User Guide 9/10. What factors do you consider to not include nonploar solvation energy for dynamic PB calculation? Can this absence of nonploar solvation energy still have reasonable and convergent MD results compared with the MD with noploar solvation energy or explicit solvent MD, that is, whether the nonpolar solvation is important or not?

Best wishes!

Jin Tao

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