From f4de94cdef175440be4b27605f61446706f5b110 Mon Sep 17 00:00:00 2001 From: Paul Bauer Date: Sat, 28 Dec 2019 11:59:13 +0100 Subject: [PATCH] Remove membed from features gmx membed currently does not work because the group scheme has been removed. Change-Id: I775ee8d2268e44610fa04ca15a1f3ff92b18f574 --- docs/user-guide/mdrun-features.rst | 111 ------------------------------------- 1 file changed, 111 deletions(-) diff --git a/docs/user-guide/mdrun-features.rst b/docs/user-guide/mdrun-features.rst index 5444f97ade..08ea83f6d8 100644 --- a/docs/user-guide/mdrun-features.rst +++ b/docs/user-guide/mdrun-features.rst @@ -141,114 +141,3 @@ simulation shortly before 2.5 hours elapse, which can be useful when running under cluster queues (as long as the queuing system does not ever suspend the simulation). -Running a membrane protein embedding simulation ------------------------------------------------ - -This is a module to help embed a membrane protein into an equilibrated -lipid bilayer at a position and orientation specified by the user. - -This method was initially described as a ProtSqueeze technique -(`Yesylevskyy S.O., J Chem Inf Model 47(5) (2007) 1986-94`_) and -later implemented in |Gromacs| as g_membed tool (`Wolf et al, J Comp Chem 31 (2010) 2169-2174`_). -Currently the functionality of g_membed is available in mdrun if -``-membed`` option is specified (see below). The current implementation as a sub-tool of mdrun is -deprecated, and may be replaced in the future, e.g. with ``gmx membed``. - -.. _Yesylevskyy S.O., J Chem Inf Model 47(5) (2007) 1986-94: https://dx.doi.org/10.1021/ci600553y -.. _Wolf et al, J Comp Chem 31 (2010) 2169-2174: http://onlinelibrary.wiley.com/doi/10.1002/jcc.21507/full - -The main advantage is that it is possible to use very complex lipid bilayers -with a number of different components that have been relaxed for a -long time in a previous simulation. In theory that could be accomplished -with a procedure similar to :ref:`gmx solvate`, but since lipids are much larger -than water molecules it will lead to a large vacuum layer between the -protein and membrane if we remove all molecules where any atom is -overlapping. Instead, this module works by first artificially shrinking -the protein in the xy-plane, then it removes lipids that overlap with -a much smaller core, after which we gradually push the protein atoms -back to their initial positions, while using normal dynamics for the -rest of the system so lipids adapt to the protein. - -To use membrane embedding, start by building a lipid bilayer that is -just-so-slightly larger in the xy-plane than what you expect to need -in the end, and make sure you have enough water outside the membrane -to accommodate globular domains. Place the protein in the same coordinate -file (and topology) as your lipid bilayer, and make sure it is in the -orientation and position you want right in the middle of the bilayer. - -The first settings have to be entered in the mdp file that controls -your simulation. You need an energy group corresponding to your -protein, this group should be frozen (all dimensions), and we should -exclude all interactions inside the protein to avoid problems when it -is distorted. For instance: - -:: - - integrator = md - energygrps = Protein - freezegrps = Protein - freezedim = Y Y Y - energygrp_excl = Protein Protein - -You will also need a number of settings for the actual membrane -embedding process. These are entered as similar name and value pairs, -but in the separate text data file ``embed.dat`` that you provide as -the argument to the ``-membed`` option (we refer to the below -when explaining the process). The embedding works in for stages: - -1. The protein is resized around its center of mass by a factor - ``xy`` in the xy-plane (the bilayer plane), and a factor ``z`` - along the z-axis (normal to the bilayer). If the height of the - protein is the same or smaller than the thickness of the - membrane, a z-fraction larger than 1.0 can prevent the protein - from being enveloped by the lipids. - -2. All lipid and solvent molecules overlapping with the resized - protein are removed. All interactions inside the protein are - turned off to prevent numerical issues for small values of the - scaling fractions. - -3. A single md step is performed, where atoms in the rest of the - system are moved. - -4. The resize factors are adjusted by the small amounts - (1-xy)/nxy and (1-z)/nz, where ``nxy`` and ``nz`` are the - number of iterations to use. The resize factor for the xy-plane - is adjusted first. The resize factor for the z-direction is not - changed until the xy factor is 1.0 (after ``nxy`` iterations). - -5. Steps 3 and 4 are repeated until the protein has again reached - its original size, i.e. after nxy+nz iterations. After the - embedding you might still want to perform a short relaxation. - -Parameters that can be specified in ``embed.dat``, with default -values that will be used if the setting is omitted: - -- ``xyinit`` (0.5) Resize factor for the protein in the xy - dimension before starting embedding. - -- ``xyend`` (1.0) Final resize factor in the xy dimension. - -- ``zinit`` (1.0) Resize factor for the protein in the z - dimension before starting embedding. - -- ``zend`` (1.0) Final resize faction in the z dimension. - -- ``nxy`` (1000) Number of iteration for the xy dimension. - -- ``nz`` (0) Number of iterations for the z dimension. - -- ``rad`` (0.22) Probe radius to check for overlap between - the group to embed and the membrane. - -- ``pieces`` (1) Perform piecewise resize. Select parts of the group - to insert and resize these with respect to their own geometrical center. - -- ``asymmetry`` (no) Allow asymmetric insertion, i.e. the number of - lipids removed from the upper and lower leaflet will not be checked. - -- ``ndiff`` (0) Number of lipids that will additionally be removed - from the lower (negative number) or upper (positive number) - membrane leaflet. - -- ``maxwarn`` (0) Largest number of membed warnings allowed. -- 2.11.4.GIT