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

[J B]

Hi,
the distance is 3.89 nm and the z-dimension is roughly 8 nm


> Date: Sat, 28 Apr 2012 09:18:31 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Umbrella sampling PMF,	drug and membrane with pull_geometry=cylinder
> 
> 
> 
> 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
> 
> -- 
> ========================================
> 
> 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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