Equilibration of the membrane-protein system done in CHARMM-GUI

From: James Starlight (jmsstarlight_at_gmail.com)
Date: Wed Nov 06 2013 - 00:51:22 CST

Dear all,

As I've mentioned I had problems with the simulation of the
protein-membrane complex made in Charm-gui. Briefly I had no problems
during all equilibration phases but on the 7.1 ptoduction run step l've
observed the diffusion of the protein as the whole (!!!) in the x-y plane
of the membrane (analysis of the RMSD provides me hight increase in RMSD
(up to 10A) during first 2ns when such 2D diffusion have been detected).
I'm not sure if this simulation was OK because I've never seen such motion
in X-Y plane (previously making long simulation in Gromacs with Langevins
dynamics and Parinello's barostat). As I've mentioned such motion is
observed during 7.1 step ( here any restraints are removed from the conf
file like
# planar restraint
colvars on
exec sed -e "s/Constant \$fc/Constant 0/g"
membrane_lipid_restraint.namd.col > restraints/$outputname.col
colvarsConfig restraints/$outputname.col

# dihedral restraint
extraBonds yes
exec sed -e "s/\$FC/0/g" restraints/dihe.txt > restraints/$outputname.dihe
extraBondsFile restraints/$outputname.dihe

Does I need more prolonged equilibration in case where I simulate protein
inserted in the membrane ( in comparison to the pure bilayer) or may be
some additional restrains should be included in the 7.1 production run as
well ?


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