Provided by: gromacs-data_4.6.5-1build1_all

**NAME**

g_dos - compute density of states from a simulation trajectoryVERSION4.5.5

**SYNOPSIS**

g_dos-ftraj.trr-stopol.tpr-nindex.ndx-vacfvacf.xvg-mvacfmvacf.xvg-dosdos.xvg-gdos.log-[no]h-[no]version-niceint-btime-etime-dttime-[no]w-xvgenum-[no]v-[no]recip-[no]abs-[no]normdos-Treal-acflenint-[no]normalize-Penum-fitfnenum-ncskipint-beginfitreal-endfitreal

**DESCRIPTION**

g_doscomputes 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. Properties based on the DoS are printed on the standard output.

**FILES**

-ftraj.trrInputFull precision trajectory: trr trj cpt-stopol.tprInputRun input file: tpr tpb tpa-nindex.ndxInput,Opt.Index file-vacfvacf.xvgOutputxvgr/xmgr file-mvacfmvacf.xvgOutputxvgr/xmgr file-dosdos.xvgOutputxvgr/xmgr file-gdos.logOutputLog file

**OTHER** **OPTIONS**

-[no]hnoPrint help info and quit-[no]versionnoPrint version info and quit-niceint19Set the nicelevel-btime0First frame (ps) to read from trajectory-etime0Last frame (ps) to read from trajectory-dttime0Only use frame when t MOD dt = first time (ps)-[no]wnoView output.xvg,.xpm,.epsand.pdbfiles-xvgenumxmgracexvg plot formatting:xmgrace,xmgrornone-[no]vyesBe loud and noisy.-[no]recipnoUse cm-1 on X-axis instead of 1/ps for DoS plots.-[no]absnoUse the absolute value of the Fourier transform of the VACF as the Density of States. Default is to use the real component only-[no]normdosnoNormalize the DoS such that it adds up to 3N. This is a hack that should not be necessary.-Treal298.15Temperature in the simulation-acflenint-1Length of the ACF, default is half the number of frames-[no]normalizeyesNormalize ACF-Penum0Order of Legendre polynomial for ACF (0 indicates none):0,1,2or3-fitfnenumnoneFit function:none,exp,aexp,exp_exp,vac,exp5,exp7,exp9orerffit-ncskipint0Skip N points in the output file of correlation functions-beginfitreal0Time where to begin the exponential fit of the correlation function-endfitreal-1Time 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 double precision).

**SEE** **ALSO**

gromacs(7)More information aboutGROMACSis available at <http://www.gromacs.org/>. Wed 21 Sep 2011 g_dos(1)