disco(1)

NAME
disco VERSION 3.2.0

SYNOPSIS
disco -g disco.log -f conf.gro -d cdist.dat -do distout.dat -c out.gro -center out.gro -n index.ndx -o structs.xtc -keep unconverged.xtc -viol vvv.pdb -[no]h -nice int -nf int -nit int -[no]v -[no]chiral -[no]pep -[no]lower -[no]weighted -[no]dump -[no]cubic -[no]explicit -[no]fit -nbcheck int -nstprint int -ranlist int -[no]ranlistfirst -lowdev real -seed int -box vector -grow int

DESCRIPTION
disco reads a topology (tpr) file and runs distance geometry calculations based on the distances defined in the distance-restraints section of the topology. An appropriate tpr file may be generated by the cdist program. The algorithm is the CONCOORD algorithm of De Groot et al., which in turn is derived from the SHAKE alogrithm. A parallel version of disco is under development whihc uses a master-slave approach. Slaves work asynchronously, and it is no problem when nodes are not equally fast, or when a node dies, unless it is the master node.

FILES
-g disco.log Output
 Log file -f conf.gro Input
 Generic structure: gro g96 pdb tpr tpb tpa xml -d cdist.dat Input
 Generic data file -do distout.dat Output, Opt.
 Generic data file -c out.gro Input
 Generic structure: gro g96 pdb xml -center out.gro Input, Opt.
 Generic structure: gro g96 pdb xml -n index.ndx Input, Opt.
 Index file -o structs.xtc Output
 Generic trajectory: xtc trr trj gro g96 pdb -keep unconverged.xtc Output, Opt.
 Generic trajectory: xtc trr trj gro g96 pdb -viol vvv.pdb Output, Opt.
 Protein data bank file

OTHER OPTIONS
-[no]h no
 Print help info and quit -nice int 19
 Set the nicelevel -nf int 10
 Number of structures to generate -nit int 1000
 Max number of iterations for a structure to converge -[no]v yes
 Be verbosive -[no]chiral yes
 Check chirality during disco-ing -[no]pep yes
 Flip all cis-peptide bonds automatically to trans -[no]lower no
 Use lower bounds only for nonbondeds. -[no]weighted no
 Use weighted disco. The STX file must be a pdb file in this case and weights are read from the occupancy field -[no]dump no
 Dump the trajectory of the shaking to testX.xtc file where X is the structure number. -[no]cubic no
 Generate coordinates in a cubic box, rather than rectangular -[no]explicit no
 Use explicit updating of positions if the sum of deviations is smaller than lowdev -[no]fit no
 Fit output structures to reference structure in tpx file -nbcheck int 1
 Check non-bonded interactions every N steps -nstprint int 1
 Print number of violations every N steps -ranlist int 0
 Update list order to avoid bias every n steps -[no]ranlistfirst yes
 Randomize list once before shaking -lowdev real 0.05
 Low deviation [Sum of distance deviation per atom in nm] beyond which nonbondeds are done every step -seed int 1997
 Seed for the random number generator -box vector 2 2 2
 Boxsize (nm) for generating random coordinates -grow int 0
 Number of steps after which Van der Waals lower bounds grow from 0 to the real lower bounds. If this is 0 (default), the Van der Waals lower bounds are in effect from the beginning