[gmx-users] Membrane-protein Simulation

Najamuddin Memon najamuddinmemon63 at gmail.com
Thu May 2 12:41:05 CEST 2019

Yes it is normal to correct .xtc file through -pbc flag

On Thu, May 2, 2019, 12:57 PM Sankaran SV . <119013033 at sastra.ac.in> wrote:

> Dear all,
> 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?
> Thanks.
> --
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