Dear Amber Users!
I am using the following cpptraj script for the periodicity
post-processing of MD trajectory computed for a membrane system
containing two monomers embedded into the lipid bilayer.
parm complex.prmtop
trajin 07_Prod_*.nc 1 -1 30
trajout stripped_traj88.pdb
strip :WAT,Na+,Cl-
center :105,201
autoimage
The issue is that the post-processed trajectory is centered on the
interphase between two monomers defined as :105,201 and visually the
membrane moves up-down :-)
Would it be rather possible to center the system onto the membrane in
order that I may avoid such an effect??
Many thanks in advance !
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Received on Tue Dec 05 2023 - 06:30:03 PST
