gmx distance calculates distances between pairs of positions as a function of time. Each selection specifies an independent set of distances to calculate.
gmx distance [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]] [-oav [<.xvg>]] [-oall [<.xvg>]] [-oxyz [<.xvg>]] [-oh [<.xvg>]] [-oallstat [<.xvg>]] [-b ] [-e ] [-dt ] [-tu <enum>] [-fgroup <selection>] [-xvg <enum>] [-...
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...
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...
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 ...
I am trying to do a simulation with distance restraints for the Zn-His(NE2)atoms in a peptide, but the distances are not kept to what I want them to be. Why? I have added this in my topology.top: ; Include Position restraint file ...
(-1)Minimum coordinate for averaging-xmax<real>(-1)Maximum coordinate for averaging-n1<int>(0)Number of grid cells in the first direction-n2<int>(0)Number of grid cells in the second direction-amax<real>(0)Maximum axial distance from the center-rmax<real>(0)Maximum radial distance-[no]...
Re: [gmx-users] Re: Minimum distance periodic images, protein simulation Mark Abraham [gmx-users] Significant slowdown in 4.6? (4.6.3) Jonathan Saboury [gmx-users] Re: Significant slowdown in 4.6? (4.6.3) Jonathan Saboury [gmx-users] g_covar average.pdb calculation Deniz Aydin Re:...
atomsArrayRef);break;caseesbRect:caseesbNone:default:break; }if(man->bPbc) {gmx_rmpbc(man->gpbc, man->natom, man->box, man->x); reset_mols(&(man->top.mols), man->box, man->x); } ncount =0; }else{if(man->nSkip >0) ...
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 ...