AMBER Archive (2009)

Subject: [AMBER] Heat and Equilibrate Hybrid GB solvent?

From: Jason A. Ford-Green (jgreen_at_ccmsi.us)
Date: Fri Jan 16 2009 - 15:14:41 CST

 All,

 Hello. I have a more technical question this time around. Should one conduct the usual 2 stage heat up and equilibrate protocol for a fully solvated protein (TIP3 waters) when preparing for a hybrid solvent REMD simulation? This is in reference to the tutorials for REMD in GB solvent and MD simulations in explicit solvent. I have yet to see a tutorial regarding hybrid solvent prep work, and the manual does not address such issues. Any help would be greatly appreciated this late in the day. Thanks!

Cheers,

Jason Ford-Green
Doctoral Student
Interdisciplinary Nanotoxicity Center
Jackson State University
Contracted Technical Service Student
U.S. Army Engineer Research and Development Center
PI: Jerzy Leszczynski,Ph.D
Cell: 850-443-9233
Lab: 601-979-1797

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