Section 1: user commands and tools
NAME xpm2ps – convert XPM (XPixelMap) file to postscript VERSION 4.0.1 SYNOPSIS xpm2ps -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…
NAME xpm2ps – convert XPM (XPixelMap) file to postscript VERSION 4.0.1 SYNOPSIS xpm2ps -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…
NAME x2top – generates a primitive topology from coordinates VERSION 4.0.1 SYNOPSIS x2top -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 DESCRIPTION x2top generates a primitive topology from a coordinate file. The program…
NAME x2top – generates a primitive topology from coordinates VERSION 4.0.1 SYNOPSIS x2top -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 DESCRIPTION x2top generates a primitive topology from a coordinate file. The program…
NAME wheel – plots helical wheels VERSION 4.0.1 SYNOPSIS wheel -f nnnice.dat -o plot.eps -[no]h -nice int -r0 int -rot0 real -T string -[no]nn DESCRIPTION wheel 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…
NAME wheel – plots helical wheels VERSION 4.0.1 SYNOPSIS wheel -f nnnice.dat -o plot.eps -[no]h -nice int -r0 int -rot0 real -T string -[no]nn DESCRIPTION wheel 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…
NAME g_wham – weighted histogram analysis after umbrella sampling VERSION 4.0.1 SYNOPSIS g_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 DESCRIPTION This is an analysis program that implements the Weighted Histogram Analysis Method (WHAM). It is intended to analyze .pdo files…
NAME g_wham – weighted histogram analysis after umbrella sampling VERSION 4.0.1 SYNOPSIS g_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 DESCRIPTION This is an analysis program that implements the Weighted Histogram Analysis Method (WHAM). It is intended to analyze .pdo files…
NAME g_velacc – calculates velocity autocorrelation functions VERSION 4.0.1 SYNOPSIS g_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 DESCRIPTION g_velacc computes the velocity autocorrelation function. When the -m…
NAME g_velacc – calculates velocity autocorrelation functions VERSION 4.0.1 SYNOPSIS g_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 DESCRIPTION g_velacc computes the velocity autocorrelation function. When the -m…
NAME g_vanhove – calculates Van Hove displacement functions VERSION 4.0.1 SYNOPSIS g_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…
NAME g_vanhove – calculates Van Hove displacement functions VERSION 4.0.1 SYNOPSIS g_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…
NAME trjorder – orders molecules according to their distance to a group VERSION 4.0.1 SYNOPSIS trjorder -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 DESCRIPTION trjorder orders molecules according to the smallest distance to atoms in…
NAME trjorder – orders molecules according to their distance to a group VERSION 4.0.1 SYNOPSIS trjorder -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 DESCRIPTION trjorder orders molecules according to the smallest distance to atoms in…
NAME trjconv – converts and manipulates trajectory files VERSION 4.0.1 SYNOPSIS trjconv -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…
NAME trjconv – converts and manipulates trajectory files VERSION 4.0.1 SYNOPSIS trjconv -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…
NAME trjcat – concatenates trajectory files VERSION 4.0.1 SYNOPSIS trjcat -f traj.xtc -o trajout.xtc -n index.ndx -demux remd.xvg -[no]h -nice int -tu enum -[no]xvgr -b time -e time -dt time -prec int -[no]vel -[no]settime -[no]sort -[no]keeplast -[no]cat DESCRIPTION trjcat concatenates several input trajectory files in sorted order. In case of double time frames the one…
NAME trjcat – concatenates trajectory files VERSION 4.0.1 SYNOPSIS trjcat -f traj.xtc -o trajout.xtc -n index.ndx -demux remd.xvg -[no]h -nice int -tu enum -[no]xvgr -b time -e time -dt time -prec int -[no]vel -[no]settime -[no]sort -[no]keeplast -[no]cat DESCRIPTION trjcat concatenates several input trajectory files in sorted order. In case of double time frames the one…
NAME g_traj – plots x, v and f of selected atoms/groups (and more) from a trajectory VERSION 4.0.1 SYNOPSIS g_traj -f traj.xtc -s topol.tpr -n index.ndx -ox coord.xvg -oxt coord.xtc -ov veloc.xvg -of force.xvg -ob box.xvg -ot temp.xvg -ekt ektrans.xvg -ekr ekrot.xvg -vd veldist.xvg -cv veloc.pdb -cf force.pdb -av all_veloc.xvg -af all_force.xvg -[no]h -nice int…
NAME g_traj – plots x, v and f of selected atoms/groups (and more) from a trajectory VERSION 4.0.1 SYNOPSIS g_traj -f traj.xtc -s topol.tpr -n index.ndx -ox coord.xvg -oxt coord.xtc -ov veloc.xvg -of force.xvg -ob box.xvg -ot temp.xvg -ekt ektrans.xvg -ekr ekrot.xvg -vd veldist.xvg -cv veloc.pdb -cf force.pdb -av all_veloc.xvg -af all_force.xvg -[no]h -nice int…