[gmx-users] lipid bilayer and umbrella sampling

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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