Hi all :
I am trying to do some MM-PB/SA calculation in my system. For equilibration
of the salivated system (octahedral TIP3P) i used the fallowing scheme-
1- Minimization of solvent molecules with fixed protein
2- Heating system with fixed protein (300 ps)
3- Equilibrating water in the system with fixed protein (700 ps)
4- Minimization of protein with with fixed water
5- Heating system with fixed water (300ps)
6- Equilibration of whole system without any restrain (10 ns)
I found that the density in the step 6 is less than 1 for first few few ps
and then it adjust is very soon. When i look in adjustment of water molecule
after each step, I found a weird thing after step 3. I did imaging with
ptraj and found that few planes of octahedral water-box have small well
shaped arrangenemt of water. I am really surprised that why this happened.
Is it may be due to only 12A layer of water box, that PBC is showing effcet
of adgacent protein ?
Reigards
..mish
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Received on Thu May 06 2010 - 05:30:03 PDT
