[gmx-users] lipid bilayer and umbrella sampling

Giovanni Mancini g_mancini at ymail.com
Mon Nov 7 17:15:45 CET 2011

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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