dipole_potential_and_esp
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dipole_potential_and_esp [2018/03/05 12:29] – 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 (position | + | **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 | ||
- | 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:// | |
- | Location of files on MARCC: | + | |
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 <chrg_dens.inp> computes the total charge density along z (the bilayer normal) in slabs of thickness 0.1 Angstroms, from -32.95 to 32.95 Angstroms. It reads in the re-centered trajectories from the current directory with file names of the form " | + | The input file "chrg_dens.inp" |
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.1520270990.txt.gz · Last modified: 2018/03/05 12:29 by edit