g_sans

VERSION 4.6.7
Fri 29 Aug 2014

This is simple tool to compute SANS spectra using Debye formula It currently uses topology file (since it need to assigne element for each atom)

Parameters:

-pr Computes normalized g(r) function averaged over trajectory

-prframe Computes normalized g(r) function for each frame

-sq Computes SANS intensity curve averaged over trajectory

-sqframe Computes SANS intensity curve for each frame

-startq Starting q value in nm

-endq Ending q value in nm

-qstep Stepping in q space

Note: When using Debye direct method computational cost increases as 1/2 * N * (N - 1) where N is atom number in group of interest

WARNING: If sq or pr specified this tool can produce large number of files! Up to two times larger than number of frames!

option	filename	type	description
`-s`	`topol.tpr`	Input	Run input file: tpr tpb tpa
`-f`	`traj.xtc`	Input	Trajectory: xtc trr trj gro g96 pdb cpt
`-n`	`index.ndx`	Input, Opt.	Index file
`-d`	`nsfactor.dat`	Input, Opt.	Generic data file
`-pr`	`pr.xvg`	Output	xvgr/xmgr file
`-sq`	`sq.xvg`	Output	xvgr/xmgr file
`-prframe`	`prframe.xvg`	Output, Opt.	xvgr/xmgr file
`-sqframe`	`sqframe.xvg`	Output, Opt.	xvgr/xmgr file

option	type	default	description
`-[no]h`	bool	`no`	Print help info and quit
`-[no]version`	bool	`no`	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)
`-tu`	enum	`ps`	Time unit: `fs`, `ps`, `ns`, `us`, `ms` or `s`
`-xvg`	enum	`xmgrace`	xvg plot formatting: `xmgrace`, `xmgr` or `none`
`-mode`	enum	`direct`	Mode for sans spectra calculation: `direct` or `mc`
`-mcover`	real	`-1`	Monte-Carlo coverage should be -1(default) or (0,1]
`-[no]pbc`	bool	`yes`	Use periodic boundary conditions for computing distances
`-startq`	real	`0`	Starting q (1/nm)
`-endq`	real	`2`	Ending q (1/nm)
`-qstep`	real	`0.01`	Stepping in q (1/nm)
`-seed`	int	`0`	Random seed for Monte-Carlo