The RMSD at time t is calculated as the RMS of the differences indistance between atom-pairsin the reference structure and the structure at time t. gmx rmsdistcan also produce matrices of therms distances, rms distances scaled with themean distanceand the mean distances and matrices with NMR ...
Option -ur sets the unit cell representation for options mol, res and atom of -pbc. All three options give different results for triclinic boxes and identical results for rectangular boxes. rect is the ordinary brick shape. tric is the triclinic unit cell. compact puts all atoms at the close...
The RMSD at time t is calculated as the RMS of the differences in distance between atom-pairs in the reference structure and the structure at time t. gmx rmsdist can also produce matrices of the rms distances , rms distances scaled with the mean distance and the mean distances and matrices...
When I look at the structure, two of the restrained His(atom 139 and 333) has left the Zn(atom 355). Some values from the distance analysis are printed below: g_dist -f traj.trr -s b4pr.tpr -n index.ndx -o dist139.xvg less dist139.xvg @ xaxis label "Time (ps)" @ yaxis l...
These dots are first checked against covalently bonded atoms to see whether any of the dots are buried. The exposed dots from the first step are then checked against a non-bonded pair list with a cutoff distance of 9 Å to see whether any of the exposed dots from the first step are ...
Maximum radial distance -[no]mirror (no) Add the mirror image below the axial axis -[no]sums (no) Print density sums (1D map) to stdout -unit <enum> (nm-3) Unit for the output: nm-3, nm-2, count -dmin <real> (0) Minimum density in output -dmax <real> (0) Maximum density...
rms 0.000303, max 0.005164 (between atoms 18949 and 18948) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 18949 18948 42.3 0.1112 0.1117 0.1111 Step 1054, time 2.108 (ps) LINCS WARNING ...
Largest distance (nm) to be considered in a cluster -[no]mol (no) Cluster molecules rather than atoms (needs .tpr file) -[no]pbc (yes) Use periodic boundary conditions -nskip <int> (0) Number of frames to skip between writing -nlevels <int> (20) Number of levels of grey in .xpm...
compact puts all atoms at the closest distance from the center of the box. This can be useful for visualizing e.g. truncated octahedra or rhombic dodecahedra. The center for options tric and compact is tric (see below), unless the option -boxcenter is set differently. Option -center ...
}/* Store the distance as the B-factor */if(bPDBout) {for(i =0; (i < nwat); i++) {for(j =0; (j < na); j++) { top.atoms.pdbinfo[order[i].i+j].bfac =std::sqrt(order[i].d2); } } } write_trx(out, natoms, swi, &top.atoms,0, t, box, x,NULL,NULL); ...