[gmx-users] Enough hydration of the channel

Aswathy ammasachu at gmail.com
Fri Jun 18 05:42:27 CEST 2010

Thank you very much.

In some papers I have seen the graph for hydration of the channel. How can
we calculate that using Gromacs ? (or any other program?)


On Thu, Jun 17, 2010 at 7:52 PM, <chris.neale at utoronto.ca> wrote:

> 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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