[gmx-users] lipid bilayer and umbrella sampling

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 7 18:37:17 CET 2011

Giovanni Mancini wrote:
> 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?

It's certainly the most immediate solution that comes to my mind.  Try it and 
see if it alleviates your issue.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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