Main Table of Contents

Fri 5 Jul 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