Analysis+tools

toc =Volumetric data=

Volumetric data represent ANY 3D property of a system, that can be presented with an isosurface: density (concentration, charge, ... ), property (orbitals, ... ). VMD presents the VolMap utility to calculate different types of concentration. Maestro provides tools for preparing different types of molecular surfaces and hydrophobic/hydrophilic surface (Maestro User Manual, p. 225)

=Electrostatic potential from charge distribution=

Slab geometry
function [xp] = potential_slab (xq,e) % INPUT: % xq - charge density with the support xq(:,1) - support in [nm], xq(:,2) - charge density in [e/nm3] % e - dielectric permitivity, usually just 1. % OUTPUT % xp - potential in [V] with the support in [nm].

% the origin is taken to be the middle of the slab. The middle of the slab % is fould as the middle point between first and last nonzero charge % density elements.

Example usage: code xp=potential_slab(xq,1); code



=Gromacs=

Charge distribution
Charge distribution across the Z direction in slab geometry.

Usage example: in this example the script will calculate the charge distributions across the Z axis for systems with name run*.tpr (mean there are files run0.tpr, run0.xtc, run1.tpr, run1.xtc ...). The output data will be stored with different suffixes in the names.

code format="bash" for i in `ls run*.tpr`; do   echo $i fn=`echo $i | sed "s/.tpr//g"`
 * 1) !/bin/bash

run=$fn b=2000 charge_slab.sh -run $run -b $b -suf "sys_${run}" -mol System,TEA,BF4,ACN -nslices 725 done

The script: code

Density profile
Calculates the density profile across the Z direction. Example usage: code dpz.sh -run run1 -b 0 -e 10000 -suf run1 -mol TEA,BF4 -bin 0.01 -rdftype mol_com -wall Wlef code



Calculate radial density profile (RDP) and its running integral
Example usage: code rdp.sh -run run1 -b 1000 -e 10000 -suf _1-10 -mol NMP,NA,I -bin 0.01 -rdftype mol_com -cnt C66 code

Calculate evolution over trajectory of radial density profile (RDP) and its running integral
Example usage: code rdp_evol.sh NMP 1 30 10 code

=Matlab=

Interpolate function
code code

Y1=change_grid2(Y0,X0,X1,left_val,right_val,dX)

where Y0 - initial values of the function on grid X0 (column vector/ vectors) X0 - grid of initial function (column vector/ vectors) X1 - grid of the interpolated function (column vector/ vectors) Y1 - values of the interpolated function (column vector/ vectors) left_val - if X1 has points, which are smaller than min(X0)-dX, the value of interpolated function in these points will be constant left_val right_val - if X1 has points, which are larger than max(X0)+dX, the value of interpolated function in these points will be constant right_val dX - by default - X0(2)-X0(1), but you may use any value (see left_val, right_val for details)

Integrate Mean force curve to get PMF


=VMD=

Surface residues
@http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/4190.html

The "buried" keyword is a shortcut that's hardwired to match various residues, and it doesn't take into account the actual structure you've got loaded. Another method that likely has more merit, would be to calculate the solvent accessible surface area, and use that as your measure of "buried" or "surface" etc. You could run a script setting the user field for each residue with its SASA, and then use a selection like "user > 1.0" or something like that as a heuristic to determine which residues are exposed and which are not. One could even do this for all of the atoms invidually, but it would take a while to calculate. Try using the "user > 1.0" with a script like this one and let me know if that helps.

mol delete all mol addfile 1o6z.pdb set allsel [atomselect top all] set residlist [lsort -unique [$allsel get resid]] foreach r $residlist { set sel [atomselect top "resid $r"] set rsasa [measure sasa 1.4 $allsel -restrict $sel] $sel set user $rsasa $sel delete puts "resdidue $r, sasa: $rsasa" } mol modcolor 0 [molinfo top] User mol colupdate 0 [molinfo top] 1 mol scaleminmax [molinfo top] 0 auto
 * 1) Example script that sets the "User" data field with SASA values
 * 1) Example script that sets the "User" data field with SASA values
 * 1) Get list of residues
 * 1) Get list of residues
 * 1) Make an atom selection, set the User field with the SASA value for
 * 2) the selected atom
 * 1) the selected atom
 * 1) change the "color by" and "trajectory" tab settings to color by SASA
 * 1) change the "color by" and "trajectory" tab settings to color by SASA