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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