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

[Justin A. Lemkul]

On 4/28/12 12:28 PM, J B wrote:
> Hi,
>
> the distance is 3.89 nm and the z-dimension is roughly 8 nm
>
>

Is the problem specific to cylinder geometry?  Do other settings work?  Does it 
make a difference if you set values for pull_r0 and pull_r1?

-Justin

>
>  > 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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>

-- 
========================================

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

========================================