[gmx-users] PMF of ligand transport

Chris Neale chris.neale at utoronto.ca
Mon May 10 18:25:17 CEST 2010

Pick a small collection of backbone atoms near the center of your channel and use them as your reference group. 
Overcome the sign problem by optimal selection of pull options (see below). pull_pbcatom values should not be important
if you select your groups as I suggest -- otherwise be sure to understand how they work.

pull                     = umbrella
pull_geometry            = position
pull_dim                 = N N Y
pull_start               = no
pull_nstxout             = 250
pull_nstfout             = 250
pull_ngroups             = 1
pull_group0              = MY_SELECTION_OF_BACKBONE_ATOMS
pull_pbcatom0            = 0
pull_group1              = LIGAND
pull_pbcatom1            = 0
pull_init1               = 0 0 THISDIST
pull_rate1               = 0
pull_k1                  = 500.0
pull_vec1                = 0 0 0


-- original message --

I think Justin meant that you have various positions of the ligand in 
the channel (from the SMD), so you don't need to make a new run to 
determine new positions in the channel. You need only new umbrella 
sampling simulations.

Yep, the movement of the particle will also matter, because if the 
particle moves much on the z-axis, the distance between the particle and 
the ligand will change. So you would want the particle fixed relative to 
the channel.
Two ideas:
Place the particle above the entrance of the channel. Pick three atoms 
from the entrance of the channel and determine the distance between the 
atoms and the particle. Then use distance_restraints or constraints with 
a 'bondlength' equal to the measured distance. If everything goes right 
the particle would stay where you placed it, since it does not interact 
with the enviroment it should not really influence your simulation (only 
through the constraints or distance_restraints).
I don't now how big your system is, but it would probably be a good idea 
to make a short test simulation, to look if the particle changes the 
system behavior.
But it's only an idea, i hope other people comment it.


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