gajim-history-manager – a tool to manage gajim(1) logs Synopsis–h [-c directory ] Descriptionis a tool to manage Po do some cleanup Pc log file of gajim(1). Use this program to delete or export logs. For more information on database logs see <https://trac.gajim.org/wiki/LogsDatabase>. Options-h –help Show help options -c –config-path directory Where to look for logs…
gacutil – Global Assembly Cache management utility. Synopsisgacutil [-user] [command] [options] Descriptiongacutil is a tool used by developers to install versioned assemblies into the system Global Assembly Cache (GAC) to become part of the assemblies that are available for all applications at runtime. Notice that they are not directly available to the compiler. The convention…
gabbi – Gabbi Documentation Gabbi tests are expressed in YAML as a series of HTTP requests with their expected response: tests: – name: retrieve root GET: / status: 200This will trigger a GET request to / on the configured host. The test will pass if the response’s status code is 200. Test StructureThe top-level tests…
xrama – shows animated Ramachandran plots VERSION 4.0.1 Synopsisxrama -f traj.xtc -s topol.tpr -[no]h -nice int -b time -e time -dt time Descriptionxrama shows a Ramachandran movie, that is, it shows the Phi/Psi angles as a function of time in an X-Window. Static Phi/Psi plots for printing can be made with g_rama. Some of the…
xrama – shows animated Ramachandran plots VERSION 4.0.1 Synopsisxrama -f traj.xtc -s topol.tpr -[no]h -nice int -b time -e time -dt time Descriptionxrama shows a Ramachandran movie, that is, it shows the Phi/Psi angles as a function of time in an X-Window. Static Phi/Psi plots for printing can be made with g_rama. Some of the…
xpm2ps – convert XPM (XPixelMap) file to postscript VERSION 4.0.1 Synopsisxpm2ps -f root.xpm -f2 root2.xpm -di ps.m2p -do out.m2p -o plot.eps -xpm root.xpm -[no]h -nice int -[no]w -[no]frame -title enum -[no]yonce -legend enum -diag enum -size real -bx real -by real -rainbow enum -gradient vector -skip int -[no]zeroline -legoffset int -combine enum -cmin real -cmax…
xpm2ps – convert XPM (XPixelMap) file to postscript VERSION 4.0.1 Synopsisxpm2ps -f root.xpm -f2 root2.xpm -di ps.m2p -do out.m2p -o plot.eps -xpm root.xpm -[no]h -nice int -[no]w -[no]frame -title enum -[no]yonce -legend enum -diag enum -size real -bx real -by real -rainbow enum -gradient vector -skip int -[no]zeroline -legoffset int -combine enum -cmin real -cmax…
x2top – generates a primitive topology from coordinates VERSION 4.0.1 Synopsisx2top -f conf.gro -o out.top -r out.rtp -[no]h -nice int -ff string -[no]v -nexcl int -[no]H14 -[no]alldih -[no]remdih -[no]pairs -name string -[no]pbc -[no]pdbq -[no]param -[no]round -kb real -kt real -kp real Descriptionx2top generates a primitive topology from a coordinate file. The program assumes all hydrogens…
x2top – generates a primitive topology from coordinates VERSION 4.0.1 Synopsisx2top -f conf.gro -o out.top -r out.rtp -[no]h -nice int -ff string -[no]v -nexcl int -[no]H14 -[no]alldih -[no]remdih -[no]pairs -name string -[no]pbc -[no]pdbq -[no]param -[no]round -kb real -kt real -kp real Descriptionx2top generates a primitive topology from a coordinate file. The program assumes all hydrogens…
wheel – plots helical wheels VERSION 4.0.1 Synopsiswheel -f nnnice.dat -o plot.eps -[no]h -nice int -r0 int -rot0 real -T string -[no]nn Descriptionwheel plots a helical wheel representation of your sequence.The input sequence is in the .dat file where the first line contains the number of residues and each consecutive line contains a residuename. Files-f…
wheel – plots helical wheels VERSION 4.0.1 Synopsiswheel -f nnnice.dat -o plot.eps -[no]h -nice int -r0 int -rot0 real -T string -[no]nn Descriptionwheel plots a helical wheel representation of your sequence.The input sequence is in the .dat file where the first line contains the number of residues and each consecutive line contains a residuename. Files-f…
g_wham – weighted histogram analysis after umbrella sampling VERSION 4.0.1 Synopsisg_wham -o profile.xvg -hist histo.xvg -[no]h -nice int -[no]w -[no]xvgr -min real -max real -bins int -[no]prof -temp real -[no]flip -tol real DescriptionThis is an analysis program that implements the Weighted Histogram Analysis Method (WHAM). It is intended to analyze .pdo files generated by mdrun…
g_wham – weighted histogram analysis after umbrella sampling VERSION 4.0.1 Synopsisg_wham -o profile.xvg -hist histo.xvg -[no]h -nice int -[no]w -[no]xvgr -min real -max real -bins int -[no]prof -temp real -[no]flip -tol real DescriptionThis is an analysis program that implements the Weighted Histogram Analysis Method (WHAM). It is intended to analyze .pdo files generated by mdrun…
g_velacc – calculates velocity autocorrelation functions VERSION 4.0.1 Synopsisg_velacc -f traj.trr -s topol.tpr -n index.ndx -o vac.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]m -[no]mol -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real Descriptiong_velacc computes the velocity autocorrelation function. When the -m option is used,…
g_velacc – calculates velocity autocorrelation functions VERSION 4.0.1 Synopsisg_velacc -f traj.trr -s topol.tpr -n index.ndx -o vac.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]m -[no]mol -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real Descriptiong_velacc computes the velocity autocorrelation function. When the -m option is used,…
g_vanhove – calculates Van Hove displacement functions VERSION 4.0.1 Synopsisg_vanhove -f traj.xtc -s topol.tpr -n index.ndx -om vanhove.xpm -or vanhove_r.xvg -ot vanhove_t.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -sqrt real -fm int -rmax real -rbin real -mmax real -nlevels int -nr int -fr int -rt real -ft int Descriptiong_vanhove computes…
g_vanhove – calculates Van Hove displacement functions VERSION 4.0.1 Synopsisg_vanhove -f traj.xtc -s topol.tpr -n index.ndx -om vanhove.xpm -or vanhove_r.xvg -ot vanhove_t.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -sqrt real -fm int -rmax real -rbin real -mmax real -nlevels int -nr int -fr int -rt real -ft int Descriptiong_vanhove computes…
trjorder – orders molecules according to their distance to a group VERSION 4.0.1 Synopsistrjorder -f traj.xtc -s topol.tpr -n index.ndx -o ordered.xtc -nshell nshell.xvg -[no]h -nice int -b time -e time -dt time -[no]xvgr -na int -da int -[no]com -r real Descriptiontrjorder orders molecules according to the smallest distance to atoms in a reference group….
trjorder – orders molecules according to their distance to a group VERSION 4.0.1 Synopsistrjorder -f traj.xtc -s topol.tpr -n index.ndx -o ordered.xtc -nshell nshell.xvg -[no]h -nice int -b time -e time -dt time -[no]xvgr -na int -da int -[no]com -r real Descriptiontrjorder orders molecules according to the smallest distance to atoms in a reference group….
trjconv – converts and manipulates trajectory files VERSION 4.0.1 Synopsistrjconv -f traj.xtc -o trajout.xtc -s topol.tpr -n index.ndx -fr frames.ndx -sub cluster.ndx -drop drop.xvg -[no]h -nice int -b time -e time -tu enum -[no]w -[no]xvgr -skip int -dt time -dump time -t0 time -timestep time -pbc enum -ur enum -[no]center -boxcenter enum -box vector -trans…