[gmx-users] Enough hydration of the channel

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Jun 17 16:22:21 CEST 2010

Determining how many waters is sufficient is a tough problem, try  
successive runs of option #3, below. As for the simpler topic of  
getting more hydration:

1. If the issue is simply getting the channel hydrated enough to  
overcome some transition from dry to wet, then run a neat water box od  
216 spc for 100 ps and extract a frame every 10 ps, then run genbox  
10x successively using each of these frames. This should give you  
massive hydration.

2. If that doesn't work, then you could add a new equilibration step  
where you posres some cap waters so that the channel can not dry out.  
This may allow SC's to equilibrate to a wet environment.

3. If the issue is that the water is still moving out, then why not do  
SMD on a water into the pore and find out where the repulsion is.

-- original message --

Hi everyone,

I have a homology model of a transporter. I want to study the ligand
transport through the channel. i have done the following steps.

1. Ligand has docked to the mouth of the channel
2.  Inserted the complex in POPC bilayer, then solvated, and equilibrated
for 4ns(with position restarint on Protein & ligand)
3. Then I saw tht there are very few wtaer inside the pore, Since this
channel is an aqueous pore, I have added water to the channel using genbox.
4. Then the complete system equilibrated for pico seconds.
5,in order to select different snap shots for SMD (want to do a multiple
SMDs with different starting structures.) I have run 1ns Production run and
selected different frames.

Suddenly I found that still there is no enough water in the pore, the water
is moving away from the channel during step 4 &5?

How can I solve this problem? Also how will I know how many water molecules
will be sufficient for the channel?

Thanks for your support.

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