AMBER Archive (2005)

Subject: AMBER: simulation with explicit water molecules

From: Ye MEI (ymei_at_itcc.nju.edu.cn)
Date: Sat Feb 19 2005 - 21:24:48 CST

Dear Amber8 users,

   I have some questions about simulation with explicit water molecules.
   I wanna know the energy difference of a water box with and without a ethanol molecule. I first add a TIP3PBOX around the ethanol with solvateoct command. Then I remove ethanol molecule from this starting structure to get the water box without ethanol. I also run sander to minimized this starting structure to get the minimized water box with ethanol. With these two structures, I want to calculate the energy difference.
   But I have several questions.
   Is TIP3PBOX the minimized structure of water when solute is absent? Does the dielectric constant between water molecules equal to 1 using explicit model? Is there any command in amber that can give the energy of these two water box?

Ye MEI
ymei_at_itcc.nju.edu.cn
2005-02-20

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