AMBER Archive (2006)

Subject: AMBER: Suitable water box

From: simon whitehead (jxl_edu06_at_yahoo.co.uk)
Date: Mon Mar 13 2006 - 06:07:48 CST

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
 
                
---------------------------------
To help you stay safe and secure online, we've developed the all new Yahoo! Security Centre.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu