g_sans

VERSION 4.6.1
Tue 5 Mar 2013

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
`-nt`	int	`48`	Number of threads to start