problem with equilibration of membrane-protein system

From: Azadeh Alavi (
Date: Sat Feb 14 2015 - 05:35:59 CST

Dear NAMD users,

I am doing a project in the field of simulations of ion channels. The
problem is that I do not know whether I should let the ions move towards
the selectivity filter (negative-charged residues) and stick to them during
the equilibration run. I have tried to equilibrate the system with a
constraint (a sphere at the center of the selectivity filter) which does
not let the ions to go into the selectivity filter in addition to the
constraint on the alpha carbons of the protein which is gradually
decreased. In that case, the pore widens and more waters go through it when
the constraint on alpha carbons becomes close to zero. Also, the
selectivity filter residues do not stay symmetrical and one or two of them
rotate a little. I myself feel that the result might not be correct since
the pore is supposed to be very narrow. But if I let the ions stick to the
selectivity filter, the situation seems to be better but this might be
problematic while doing the SMD or ABF simulations when only one ion is
allowed to enter the pore and after some simulation time the pore might

Any help or suggestions will be greatly appreciated. Thanks a lot for your


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