[gmx-users] Membrane-protein Simulation
Sankaran SV .
119013033 at sastra.ac.in
Thu May 2 09:57:45 CEST 2019
We are investigating the hydration dynamics of membrane proteins (AQP
embedded in DPPC membrane). The topology and the mdp files for simulations
was obtained from the MemprotMD database (mdp file:
http://memprotmd.bioch.ox.ac.uk/). We modified the temperature of
simulation to 310 K since we are interested in the hydration dynamics at
body temperature. After 100 ns simulations, we observe that the protein has
drifted from the center of the bilayer to the periphery. There was no
changes in the lipid layers. The apparent movement of the protein vanished
after pbc correction was performed with centering the protein. Could you
please advise if it is common to observe proteins drifting during the
simulation and if it is fine to correct it with pbc correction?
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