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: jalem...@vt.edu
> To: gmx-users@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
========================================
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