i have a large protein-dna complex for md simulation using amber 6.
after adding water box and neutralizing ions, i used the following
protocol for equilibration: 1. 5000 steepest descent minimization with
solute fixed. 2. 20 ps md at 10K with 25 kcal/mol restrain on solute. 3.
heat up the system for 20 ps from 10k to 300k with 25 kcal/mol restrain.
4. 100 ps md at 300k. with restrain again.
i found that the density of system is not reaching ~1 g/cc in the
equilibration process which usually happens very early in the
equilibration of dna simulation. the initial density right after adding
water box is about 0.85.
and in the equilibration, the density stabilizes at ~0.9.
i was wondering what would cause this and what would be the alternative to
do the equilibration to avoid this... thanks for any suggestions... frank
Received on Tue Aug 21 2001 - 09:38:35 PDT
