[gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

[Justin A. Lemkul]

On 4/28/12 5:12 AM, J B wrote:
> Hi.
>
> I am trying to the the PMF of transferring a drug molecule from the aqueous
> phase to a lipid bilayer.
>
> In order to minimize the effects of membrane undulations I tried to use
> pull_geometry=cylinder.
>
> Whenever I run a short simulation with umbrella sampling starting from a
> configuration with the drug molecule way above the bilayer
> the drug molecule is pulled into the bilayer rather rapidly. It appears as if
> the distance between the cylinder's COM and
> the drug molecule's COM is supposed to be zero since it is pulled to the center
> of the membrane.
>
> Since I apply an umbrella potential I find this weird and I would of course like
> the molecule to
> "stay put" at that current z-position. Probably I set up the pull code wrong.
> Here are my options:
>
> pull = umbrella
> pull_geometry = cylinder
> pull_dim = N N Y
> pull_ngroups = 1
> pull_rate1 = 0.0
> pull_k1 = 1000
> pull_start = yes
> pull_init1 = 0.0
> pull_vec1 = 0.0 0.0 1.0
> pull_pbcatom0 = 0
> pull_ngroups = 1
> pull_group0 = DPPC
> pull_group1 = drug
>
> Have not decided the radii of the cylinder yet, but that is besides the point here.
>
> I run with the 4.5.5 version and cannot figure what the problem is.
>

What is the initial distance between the drug and membrane, as measured by 
g_dist?  What is the length of your unit cell along the z-axis?

-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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