From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Tue Jun 06 2017 - 16:13:08 CDT
I am trying to do umbrella Sampling of a protein-lipid system. I have
created several windows by putting the protein at different distance along
z-axis from the lipid and equilibrated each system restraining the center
of mass of both protein and lipid.
Now I am trying to run the simulation for each window. Should I restrain
all the coordinates (x, y, z) of the center of mass of the protein and
lipid or just only z coordinate? I have seen some posts here where they
restrain all coordinates of center of mass while in some post, they said
only to restrain z coordinate.
In the configuration file from NAMD tutorial, they also restrain the z
coordinates using constraints by applying force to some selected atoms. Is
it necessary if I already restrain the coordinates in colvar file?
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