#################################################################################################### ### Dipole Analyser for VMD :: Probe systems for their dipole orientations and magnitudes. ### ### Written in TCL/TK to work with VMD. ### ### ### ### ### ### Funding gratefully provided by Unilever plc and University of Southampton. ### ### ### ### All code is "as is" and there is no implied warranty. ### ### ### ### Donovan (2012) ### ### ### #################################################################################################### What you need to run --------------------- 1. VMD 2. The code package File structure -------------- ___________________________________________________________________________________________________ |<Input files> | | |_________________________|_________________________________________________________________________| |dipole.tcl |TCL code for measuring a dipole for a defined cluster of atoms in an | | |atomistic or coarse-grained simulation. Run in conjunction with VMD | | |to analyse trajectories for given systems. Make sure in the code you | | |specify the atoms of interest (see below). | | | | |_________________________|_________________________________________________________________________| |md.xtc |This is the portable format for trajectories from gromacs. It contains | | |positional information on the molecules. | |_________________________|_________________________________________________________________________| |md.gro |This is a fixed-column coordinate file format first used in the GROMOS | | |simulation package. | |_________________________|_________________________________________________________________________| |md.psf |Crucial for the calculation of the dipoles - charges must be read in and | | |we either use a pre-generated or custom generated version of the .psf to | | |supply those charges. We enlose some simple code in the Python folder to | | |assist with conversion between PS to PSF files. |___________________________________________________________________________________________________| |<Output files> | | |_________________________|_________________________________________________________________________| |amide.txt |The output histogram of dipole orientation using cos(theta) as the | | |order parameter. You can rename this whatever that you like in the code. | | | | |_________________________|_________________________________________________________________________| What the code does ------------------ Often in simulations we want to understand the orientation and magnitudes of dipoles. This code groups up atoms (user definable) into clusters and then performs basic statistical analysis on the computed dipole to give values for the magnitude and direction of these dipoles. This may be useful in understanding countless interactions and physical behaviour. The code was designed for lipid systems but that does not mean it will not work with other systems - you simply have specific the atomic groups that you are interested in. We have used as your base system the ceramide lipid which is composed into groups - the head groups having dipoles which we loosely name: amide and glycerol for housekeeping. Running the code ---------------- 1. You must put in details of the atoms you want to examine in the code. These are currently named: amide and glycerol. You can rename these or pick up the atoms of interest and put these back in the code. set amide [atomselect top "name C25 N23 H24 O26 and (resid $i)" frame $frame] set glycerol [atomselect top "name C19 C16 C15 C14 C20 O21 H22 and (resid $i)" frame $frame] 2. You must specify which grouping to look at in the following lines: set dipa [measure dipole $amide -debye] This means you will only compute one dipole at a time over a number of frames but you can easily change this if you so desire to incorporate more than one measurement simultaneously. 3. Open VMD with your files. For example: vmd md.xtc md.gro md.psf 4. Copy and paste the code into the VMD TCL window or run in the usual way.