[gmx-users] Enough hydration of the channel

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 18 06:00:18 CEST 2010

Aswathy wrote:
> 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?)

Have a look at some of Oliver Beckstein's programs:


There are several that might be useful to you.


> Regards,
> -Aswathy
> On Thu, Jun 17, 2010 at 7:52 PM, <chris.neale at utoronto.ca 
> <mailto: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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> -- 
> Aswathy


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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