dipole_potential_and_esp
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
dipole_potential_and_esp [2018/03/05 12:24] – edit | dipole_potential_and_esp [2023/08/14 09:02] (current) – admin | ||
---|---|---|---|
Line 1: | Line 1: | ||
- | **Calculate electrostatic potential of a bilayer with respect to z (position | + | **Calculate electrostatic potential of a bilayer with respect to //z//** |
- | Location of files on DT2: /a/fs-3/export/home/deepthought2/aleonar2/ | + | This wiki explains how to calculate the total electrostatic potential of a bilayer with respect to position |
- | Location of files on MARCC: | + | |
- | | + | * Location of files on ZT1: /afs/shell.umd.edu/project/energybio/shared/jbklauda/ |
- | 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 <dyn@NFIL-recenter.dcd>. The script is set up to read inputs and trajectories from the current directory. | + | * Matlab is available for free download through TERPware: https:// |
+ | |||
+ | 1. | ||
+ | The input file "chrg_dens.inp" | ||
First update the inputs to suit your system: | First update the inputs to suit your system: | ||
* Topology file: | * Topology file: | ||
Line 12: | Line 16: | ||
* Last trajectory file number: In line 80, you can change “100”: “if nfil .le. 100 goto lp1” | * Last trajectory file number: In line 80, you can change “100”: “if nfil .le. 100 goto lp1” | ||
And, in the file < | And, in the file < | ||
+ | |||
Data file: “chrg_dens.dat” | Data file: “chrg_dens.dat” | ||
- | The data file produced by <chrg_dens.inp> will be called “chrg_dens.dat”. This file has two columns. The first column is the beginning of the z slab (of width 0.1 Angstrom) and the second column is the electron density computed in a frame. This file will be very large. | + | |
- | | + | The data file produced by "chrg_dens.inp" |
- | The script | + | |
+ | 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", and units of this vector are Volts. | ||
dipole_potential_and_esp.1520270690.txt.gz · Last modified: 2018/03/05 12:24 by edit