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
--
========================================
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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