AMBER: Suitable water box

From: simon whitehead <>
Date: Mon, 13 Mar 2006 12:07:48 +0000 (GMT)

Dear Amber users,
 I am attempting to run MD simulations (have a few basic questions about protein dynamics) on a rather protein complex (about 13000 atoms) which is L-shaped but am not sure about how to go about solvating it. I am concerned about the number of waters required but want to ensure that there is a sufficient buffer of solvent between the protein and the boundaries of the box. What is a suitable distance and does this have a bearing on what you set the electrostatic cutoff to? There are a number of solvent models and am not sure which is best, TIP3P, TIP4P or TIP5P for example? As the complex is l-shaped i am concerned that during the time frame of the simulation the complex may rotate allowing cross periodic-box interactions, is the rectangular or the octahedral box more appropriate?
 Many thanks
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Received on Sun Mar 19 2006 - 06:10:07 PST
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