[gmx-users] water passage during simulation

Justin A. Lemkul jalemkul at vt.edu
Sun Oct 16 05:17:00 CEST 2011

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 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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