AMBER Archive (2006)

Subject: Re: AMBER: Suitable water box

From: Jianzhong Liu (zhong_at_udel.edu)
Date: Mon Mar 13 2006 - 10:20:52 CST

According to my feeling, I think TIP3P is better.

Jianzhong Liu
Chemistry & Biochemistry
University of Delaware
Newark, DE 19716
Tel: 302-831-3522(O)
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             Vita Brevis, Ars Longa
  ----- Original Message -----
  From: simon whitehead
  To: amber_at_scripps.edu
  Sent: Monday, March 13, 2006 7:07 AM
  Subject: AMBER: Suitable water box

  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

  JL

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