dipole_potential_and_esp
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dipole_potential_and_esp [2018/03/05 12:46] – edit | dipole_potential_and_esp [2023/08/14 09:02] (current) – admin | ||
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- | **Calculate electrostatic potential of a bilayer with respect to z** | + | **Calculate electrostatic potential of a bilayer with respect to //z//** |
+ | This wiki explains how to calculate the total electrostatic potential of a bilayer with respect to position in //z//. The dipole potential drop can then be found by subtracting the electrostatic potential of bulk water from the potential at the center of the bilayer. (Using the scripts provided, the electrostatic potential is defined as zero at the center of the bilayer.) | ||
- | Location of files on DT2: /a/fs-3/export/home/deepthought2/aleonar2/ | + | * Location of files on ZT1: /afs/shell.umd.edu/project/energybio/shared/jbklauda/ |
- | + | * Matlab is available for free download through TERPware: https://terpware.umd.edu/Windows | |
- | Location of files on MARCC: /home-1/aleonar2@umd.edu/epp_bilayer | + | |
1. Submit “chrg_dens.inp” using the submission file “chrg_dens.csh”. | 1. Submit “chrg_dens.inp” using the submission file “chrg_dens.csh”. | ||
- | The input file " | + | The input file " |
First update the inputs to suit your system: | First update the inputs to suit your system: | ||
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Data file: “chrg_dens.dat” | Data file: “chrg_dens.dat” | ||
- | The data file produced by " | + | The data file produced by " |
2. Use Matlab script “epp_bilayer.m” to process data file “chrg_dens.dat”. | 2. Use Matlab script “epp_bilayer.m” to process data file “chrg_dens.dat”. | ||
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The script " | The script " | ||
- | The vector containing the electrostatic potential relative to the bilayer center is “epp_dppc1”. | + | The vector containing the electrostatic potential relative to the bilayer center is “epp_dppc1", and units of this vector are Volts. |
dipole_potential_and_esp.1520271960.txt.gz · Last modified: 2018/03/05 12:46 by edit