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Hi,<div><br></div><div>the distance is 3.89 nm and the z-dimension is roughly 8 nm</div><div><br></div><div><br><br><div><div id="SkyDrivePlaceholder"></div>> Date: Sat, 28 Apr 2012 09:18:31 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder<br>> <br>> <br>> <br>> On 4/28/12 5:12 AM, J B wrote:<br>> > Hi.<br>> ><br>> > I am trying to the the PMF of transferring a drug molecule from the aqueous<br>> > phase to a lipid bilayer.<br>> ><br>> > In order to minimize the effects of membrane undulations I tried to use<br>> > pull_geometry=cylinder.<br>> ><br>> > Whenever I run a short simulation with umbrella sampling starting from a<br>> > configuration with the drug molecule way above the bilayer<br>> > the drug molecule is pulled into the bilayer rather rapidly. It appears as if<br>> > the distance between the cylinder's COM and<br>> > the drug molecule's COM is supposed to be zero since it is pulled to the center<br>> > of the membrane.<br>> ><br>> > Since I apply an umbrella potential I find this weird and I would of course like<br>> > the molecule to<br>> > "stay put" at that current z-position. Probably I set up the pull code wrong.<br>> > Here are my options:<br>> ><br>> > pull = umbrella<br>> > pull_geometry = cylinder<br>> > pull_dim = N N Y<br>> > pull_ngroups = 1<br>> > pull_rate1 = 0.0<br>> > pull_k1 = 1000<br>> > pull_start = yes<br>> > pull_init1 = 0.0<br>> > pull_vec1 = 0.0 0.0 1.0<br>> > pull_pbcatom0 = 0<br>> > pull_ngroups = 1<br>> > pull_group0 = DPPC<br>> > pull_group1 = drug<br>> ><br>> > Have not decided the radii of the cylinder yet, but that is besides the point here.<br>> ><br>> > I run with the 4.5.5 version and cannot figure what the problem is.<br>> ><br>> <br>> What is the initial distance between the drug and membrane, as measured by <br>> g_dist? What is the length of your unit cell along the z-axis?<br>> <br>> -Justin<br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br></div></div> </div></body>
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