[gmx-users] Enough hydration of the channel

Aswathy ammasachu at gmail.com
Thu Jun 17 15:51:27 CEST 2010

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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