Hi.
I am trying to the the PMF of transferring a drug molecule from the aqueous
phase to a lipid bilayer.
In order to minimize the effects of membrane undulations I tried to use
pull_geometry=cylinder.
Whenever I run a short simulation with umbrella sampling starting from a
configuration with the drug molecule way above the bilayerthe drug molecule is
pulled into the bilayer rather rapidly. It appears as if the distance between
the cylinder's COM and the drug molecule's COM is supposed to be zero since it
is pulled to the center of the membrane.
Since I apply an umbrella potential I find this weird and I would of course
like the molecule to"stay put" at that current z-position. Probably I set up
the pull code wrong. Here are my options:
pull = umbrellapull_geometry = cylinderpull_dim
= N N Ypull_ngroups = 1pull_rate1 = 0.0pull_k1
= 1000pull_start = yespull_init1 = 0.0pull_vec1
= 0.0 0.0 1.0pull_pbcatom0 = 0pull_ngroups = 1pull_group0
= DPPCpull_group1 = drug
Have not decided the radii of the cylinder yet, but that is besides the point
here.
I run with the 4.5.5 version and cannot figure what the problem is.
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