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: 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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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