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packing_defects
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| ==== Packing Defect Analysis Overview ==== | ==== Packing Defect Analysis Overview ==== | ||
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| + | **Please Cite Source**: Wildermuth, K.; Monje-Galvan, | ||
| This analysis focuses on the study of membrane lipid packing defects -- areas of low density lipid packing on the surface of a membrane that expose the nonpolar core of the membrane. Packing defects arise from dispersion of membrane constituents due to external forces such as imposed surface tensions or chemical interactions with other molecules. The analysis of packing defects is useful when quantifying the membrane surface is of interest. For example, I used packing defect quantification to describe the dynamic binding event between the Osh4 ALPS-like peptide and a membrane surface, and to describe the effects of using the HMMM simulation technique. | This analysis focuses on the study of membrane lipid packing defects -- areas of low density lipid packing on the surface of a membrane that expose the nonpolar core of the membrane. Packing defects arise from dispersion of membrane constituents due to external forces such as imposed surface tensions or chemical interactions with other molecules. The analysis of packing defects is useful when quantifying the membrane surface is of interest. For example, I used packing defect quantification to describe the dynamic binding event between the Osh4 ALPS-like peptide and a membrane surface, and to describe the effects of using the HMMM simulation technique. | ||
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| - **DCD trajectory file:** 1 DCD file containing the trajectory to be analyzed. It is recommended to use a DCD with a frame count corresponding to the number of images desired to be outputted (use [[merge DCD]]), although there are parameters available in this script for skipping frames in the DCD. | - **DCD trajectory file:** 1 DCD file containing the trajectory to be analyzed. It is recommended to use a DCD with a frame count corresponding to the number of images desired to be outputted (use [[merge DCD]]), although there are parameters available in this script for skipping frames in the DCD. | ||
| - **PSF file:** associated PSF file for the trajectory. | - **PSF file:** associated PSF file for the trajectory. | ||
| - | - **[[Defect_tachyon_scav.tcl]]:** script called on by VMD | + | - **[[defect_tachyon_scav.tcl]]:** script called on by VMD |
| - | - **[[Defect_tachyon.csh]]:** c-shell script to submit job with SLURM and call VMD (default setup for DT1 operation) | + | - **[[defect_tachyon.csh]]:** c-shell script to submit job with SLURM and call VMD (default setup for DT1 operation) |
| ===Output files=== | ===Output files=== | ||
packing_defects.1495421720.txt.gz · Last modified: 2017/05/21 22:55 by edit