g_dos(1) [debian man page]
g_dos(1) GROMACS suite, VERSION 4.5.5 g_dos(1) NAME
g_dos - compute density of states from a simulation trajectory VERSION 4.5.5 SYNOPSIS
g_dos -f traj.trr -s topol.tpr -n index.ndx -vacf vacf.xvg -mvacf mvacf.xvg -dos dos.xvg -g dos.log -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]v -[no]recip -[no]abs -[no]normdos -T real -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real DESCRIPTION
g_dos computes the Density of States from a simulation. In order for this to be meaningful the velocities must be saved in the trajectory with sufficiently high frequency such as to cover all vibrations. For flexible systems that would be around a few fs between saving. Prop- erties based on the DoS are printed on the standard output. FILES
-f traj.trr Input Full precision trajectory: trr trj cpt -s topol.tpr Input Run input file: tpr tpb tpa -n index.ndx Input, Opt. Index file -vacf vacf.xvg Output xvgr/xmgr file -mvacf mvacf.xvg Output xvgr/xmgr file -dos dos.xvg Output xvgr/xmgr file -g dos.log Output Log file OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -[no]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]vyes Be loud and noisy. -[no]recipno Use cm-1 on X-axis instead of 1/ps for DoS plots. -[no]absno Use the absolute value of the Fourier transform of the VACF as the Density of States. Default is to use the real component only -[no]normdosno Normalize the DoS such that it adds up to 3N. This is a hack that should not be necessary. -T real 298.15 Temperature in the simulation -acflen int -1 Length of the ACF, default is half the number of frames -[no]normalizeyes Normalize ACF -P enum 0 Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3 -fitfn enum none Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9 or erffit -ncskip int 0 Skip N points in the output file of correlation functions -beginfit real 0 Time where to begin the exponential fit of the correlation function -endfit real -1 Time where to end the exponential fit of the correlation function, -1 is until the end KNOWN PROBLEMS
- This program needs a lot of memory: total usage equals the number of atoms times 3 times number of frames times 4 (or 8 when run in dou- ble precision). SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Wed 21 Sep 2011 g_dos(1)
Check Out this Related Man Page
g_angle(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_angle(1) NAME
g_angle - calculates distributions and correlations for angles and dihedrals VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_angle -f traj.xtc -n angle.ndx -od angdist.xvg -ov angaver.xvg -of dihfrac.xvg -ot dihtrans.xvg -oh trhisto.xvg -oc dihcorr.xvg -or traj.trr -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -type enum -[no]all -binwidth real -[no]periodic -[no]chandler -[no]avercorr -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real DESCRIPTION
g_angle computes the angle distribution for a number of angles or dihedrals. This way you can check whether your simulation is correct. With option -ov you can plot the average angle of a group of angles as a function of time. With the -all option the first graph is the average, the rest are the individual angles. With the -of option, g_angle also calculates the fraction of trans dihedrals (only for dihedrals) as function of time, but this is proba- bly only fun for a selected few. With option -oc a dihedral correlation function is calculated. It should be noted that the index file should contain atom-triples for angles or atom-quadruplets for dihedrals. If this is not the case, the program will crash. With option -or a trajectory file is dumped containing cos and sin of selected dihedral angles which subsequently can be used as input for a PCA analysis using g_covar. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -n angle.ndx Input Index file -od angdist.xvg Output xvgr/xmgr file -ov angaver.xvg Output, Opt. xvgr/xmgr file -of dihfrac.xvg Output, Opt. xvgr/xmgr file -ot dihtrans.xvg Output, Opt. xvgr/xmgr file -oh trhisto.xvg Output, Opt. xvgr/xmgr file -oc dihcorr.xvg Output, Opt. xvgr/xmgr file -or traj.trr Output, Opt. Trajectory in portable xdr format OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -[no]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -type enum angle Type of angle to analyse: angle, dihedral, improper or ryckaert-bellemans -[no]allno Plot all angles separately in the averages file, in the order of appearance in the index file. -binwidth real 1 binwidth (degrees) for calculating the distribution -[no]periodicyes Print dihedral angles modulo 360 degrees -[no]chandlerno Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi -60 or phi 60. -[no]avercorrno Average the correlation functions for the individual angles/dihedrals -acflen int -1 Length of the ACF, default is half the number of frames -[no]normalizeyes Normalize ACF -P enum 0 Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3 -fitfn enum none Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9 or erffit -ncskip int 0 Skip N points in the output file of correlation functions -beginfit real 0 Time where to begin the exponential fit of the correlation function -endfit real -1 Time where to end the exponential fit of the correlation function, -1 is until the end KNOWN PROBLEMS
- Counting transitions only works for dihedrals with multiplicity 3 SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_angle(1)