you don't say the most important thing- did you use NVT or NPT in each
step? and when you say "fixed", do you mean frozen or restrained?
On Thu, May 6, 2010 at 8:00 AM, mish <smncbr.gmail.com> wrote:
> 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 - 05:30:05 PDT
