dipole_potential_and_esp
Differences
This shows you the differences between two versions of the page.
Next revision | Previous revision | ||
dipole_potential_and_esp [2018/03/02 11:25] – created admin | dipole_potential_and_esp [2023/08/14 09:02] (current) – admin | ||
---|---|---|---|
Line 1: | Line 1: | ||
- | test | + | **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 ZT1: / | ||
+ | * Matlab is available for free download through TERPware: https:// | ||
+ | |||
+ | 1. Submit “chrg_dens.inp” using the submission file “chrg_dens.csh”. | ||
+ | The input file " | ||
+ | |||
+ | First update the inputs to suit your system: | ||
+ | * Topology file: | ||
+ | * Protein structure file: | ||
+ | * Coordinate file: | ||
+ | * Thickness of box at start of simulation (“A”): | ||
+ | * First trajectory file number: | ||
+ | * Last trajectory file number: In line 80, you can change “100”: “if nfil .le. 100 goto lp1” | ||
+ | And, in the file < | ||
+ | |||
+ | Data file: “chrg_dens.dat” | ||
+ | |||
+ | The data file produced by " | ||
+ | |||
+ | 2. Use Matlab script “epp_bilayer.m” to process data file “chrg_dens.dat”. | ||
+ | |||
+ | The script " | ||
+ | |||
+ | The vector containing the electrostatic potential relative to the bilayer center is “epp_dppc1", |
dipole_potential_and_esp.1520007928.txt.gz · Last modified: 2018/03/02 11:25 by admin