[gmx-users] water passage during simulation

[Justin A. Lemkul]

madhumita das wrote:
> Hi GROMACS users,
> 
> 
> I have done simulation of a membrane protien named aquaporin5 which 
> transports water across the membrane. I have done simulation of 3 ns and 
> want to pass water molecules during simulation. Is it possible to do in 
> GROMACS? I want to know how to do?
>                   

3 ns is far too short of a timeframe to see this type of activity spontaneously. 
  You may need tens or hundreds of ns.  You can force water through the channel 
with the pull code, but I would suggest you refer to the literature to see what 
others have done; you are not the first to try to get water or small molecules 
to move through transport proteins.

-Justin 


-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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