Main Table of Contents

Wed 13 Nov 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)


-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!


-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

Other options

-[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