[gmx-users] lipid bilayer and umbrella sampling

Chris Neale chris.neale at utoronto.ca
Mon Nov 7 20:27:22 CET 2011

If you add position restraints to your DPPC molecules, then you are 
changing your effective order parameter. The PMF for the solute along 
the normal to a restrained bilayer will have a different shape than a 
PMF for the solute along the normal to an urestrained bilayer. Whether 
or not this is a problem will depend on the question that you are trying 
to answer.

If the bilayer is falling apart, then you certainly need to do 
something. But if it is just locally ordering/disordering, then I don't 
see the big problem, besides the effect that this has on convergence 
(DOI: 10.1021/ct200316w).


-- original message --

Dear Gromacs Users,

     I am trying to extract the potential of mean force of a small 
molecule in a DPPC bilayer. To this end, I applied the methodology 
described in an online manual written by Justin Lemkul. My problem is 
when I run biasing simulations of the molecule near the interface 
(DPPC/water), some lipid molecules move to the water phase. This has as 
a consequence a local disorder of the bilayer. Below is the parameters I 
employ for the pull code:

pull                     = umbrella
pull_geometry            = distance
pull_dim                 = N N Y
pull_start               = yes
pull_ngroups             = 1
pull_group0              = DPPC
pull_group1              = DTC
pull_rate1               = 0.0
pull_k1                  = 1000

Is the position restraints on DPPC molecules a solution to my problem?
Thanks in advance

Best regards


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