From: Frances Leung (frances_leung_at_rogers.com)
Date: Mon Jan 19 2004 - 20:10:59 CST
Hello All,
I'm working on a protein complex that is of the size of about 300,000
atoms when it's solvated. The protein complex itself has around 20,000
atoms, water molecules thus take up most of the system. I'm in the
process of annealing and equilibration and it's taking really long. It
took more than 5 hrs to do 5000 steps for minimization. I know that the
solvent model can actually be created implicitly to drastically reduce
computation time, has anyone created an implicit solvent model in NAMD
before? If so, how much faster is that compared to an explicit solvent
model and how easy it is to implement in NAMD?
Frances
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