DESCRIPTION:
trjVoronoi computes the atomic Voronoi volumes and surfaces of a molecular dynamic trajectory written in .dcd or .xtc format. It requires a .pdb file containing the coordinates of the whole system, including waters and ions. If the numbers of atoms in the .pdb and trajectory files differ, the program *fails*.
The syntax of trjVoronoi is the following:
trjVoronoi -xtc myTraj.xtc -pdb myTraj.pdb -o myTraj.out -b 0 -e 20 -select "Prot Water Ions" -solute Prot -shell -parea -clusOPTIONS:
Usage: trjVoronoi -dcd file.dcd -xtc file.xtc -pdb file.pdb -o fileout - b No. First Frame -e No. Last Frame -skip No. skipped frames -hyd // Include hydrogens in Voronoi -nohyd // Do not include hydrogens in Voronoi [default] -del // Delete temporary files in MPI runs [default] -nodel // Do not delete temporary files in MPI runs -rd // Use atomic radii in the Voronoi calculation [default]* -nord // Do not use atomic radii in the Voronoi calculation -solute <string selection> Define the residue of the solute to be used in the Voronoi analysis. -test // compute total volume from Voronoi or simulation cell parameters -help // write some on line help -pvol // Print volume -parea // Print area -det filename// Define the polar segment of a detergent residue The file filename contains two strings: i) the first string is the name of the detergent residue ii)the second string contains the polar atoms of the residue *Important*: The polar atoms in the pdb and topology *MUST* all occur before the hydrophobic atoms. -detP <string>// Define a name for the polar segment of a detergent residue -detO <string>// Define a name for the hydrophobic segment of a detergent residue -shell [2]<int n>// Compute number and average volume of the n-shell water neighbours around solute -clust <float cutoff [0.0] in Angstroems> Do clustering by percolation of the solute. This is used to compute the surfaces and volumes of each cluster. If the cutoff is zero, the default, the cutoff is chosen according to the Lennard-Jones sigma parameters multiplied by an offset factor of 1.5 Default values in square bracketsdouble rd[]= {0.03, 0.175, 0.165, 0.155, 0.176, 0.12, 0.202, 0.105, 0.12};string elem[]={"H" ,"C" ,"N" ,"O" ,"S" ,"NA","CL" ,"MG" ,"CA"};