AMBER Archive (2009)
Subject: [AMBER] Heat and Equilibrate Hybrid GB solvent?
From: Jason A. Ford-Green (jgreen_at_ccmsi.us)
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!