IMPLEMENTATIONS TO GROMITA 1.06

Compatible with Gromacs version 4 (yellow highlighted)

mdrun – 4

No.	option	filename	type	description
1	-s	topol.tpr	Input	Run input file: tpr tpb tpa
2	-o	traj.trr	Output	Full precision trajectory: trr trj cpt
3	-x	traj.xtc	Output, Opt.	Compressed trajectory (portable xdr format)
4	-cpi	state.cpt	Input, Opt.	Checkpoint file
5	-cpo	state.cpt	Output, Opt.	Checkpoint file
6	-c	confout.gro	Output	Structure file: gro g96 pdb
7	-e	ener.edr	Output	Energy file: edr ene
8	-g	md.log	Output	Log file
9	-dgdl	dgdl.xvg	Output, Opt.	xvgr/xmgr file
10	-field	field.xvg	Output, Opt.	xvgr/xmgr file
11	-table	table.xvg	Input, Opt.	xvgr/xmgr file
12	-tablep	tablep.xvg	Input, Opt.	xvgr/xmgr file
13	-tableb	table.xvg	Input, Opt.	xvgr/xmgr file
14	-rerun	rerun.xtc	Input, Opt.	Trajectory: xtc trr trj gro g96 pdb cpt
15	-tpi	tpi.xvg	Output, Opt.	xvgr/xmgr file
16	-tpid	tpidist.xvg	Output, Opt.	xvgr/xmgr file
17	-ei	sam.edi	Input, Opt.	ED sampling input
18	-eo	sam.edo	Output, Opt.	ED sampling output
19	-j	wham.gct	Input, Opt.	General coupling stuff
20	-jo	bam.gct	Output, Opt.	General coupling stuff
21	-ffout	gct.xvg	Output, Opt.	xvgr/xmgr file
22	-devout	deviatie.xvg	Output, Opt.	xvgr/xmgr file
23	-runav	runaver.xvg	Output, Opt.	xvgr/xmgr file
24	-px	pullx.xvg	Output, Opt.	xvgr/xmgr file
25	-pf	pullf.xvg	Output, Opt.	xvgr/xmgr file
26	-mtx	nm.mtx	Output, Opt.	Hessian matrix
27	-dn	dipole.ndx	Output, Opt.	Index file

Other options

No.	option	type	default	description
1	-[no]h	bool	no	Print help info and quit
2	-nice	int	19	Set the nicelevel
3	-deffnm	string		Set the default filename for all file options
4	-[no]xvgr	bool	yes	Add specific codes (legends etc.) in the output xvg files for the xmgrace program
5	-[no]pd	bool	no	Use particle decompostion
6	-dd	vector	0 0 0	Domain decomposition grid, 0 is optimize
7	-npme	int	-1	Number of separate nodes to be used for PME, -1 is guess
8	-ddorder	enum	interleave	DD node order: interleave, pp_pme or cartesian
9	-[no]ddcheck	bool	yes	Check for all bonded interactions with DD
10	-rdd	real	0	The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates
11	-rcon	real	0	Maximum distance for P-LINCS (nm), 0 is estimate
12	-dlb	enum	auto	Dynamic load balancing (with DD): auto, no or yes
13	-dds	real	0.8	Minimum allowed dlb scaling of the DD cell size
14	-[no]sum	bool	yes	Sum the energies at every step
15	-[no]v	bool	no	Be loud and noisy
16	-[no]compact	bool	yes	Write a compact log file
17	-[no]seppot	bool	no	Write separate V and dVdl terms for each interaction type and node to the log file(s)
18	-pforce	real	-1	Print all forces larger than this (kJ/mol nm)
19	-[no]reprod	bool	no	Try to avoid optimizations that affect binary reproducibility
20	-cpt	real	15	Checkpoint interval (minutes)
21	-[no]append	bool	no	Append to previous output files when restarting from checkpoint
22	-maxh	real	-1	Terminate after 0.99 times this time (hours)
23	-multi	int	0	Do multiple simulations in parallel
24	-replex	int	0	Attempt replica exchange every # steps
25	-reseed	int	-1	Seed for replica exchange, -1 is generate a seed
26	-[no]glas	bool	no	Do glass simulation with special long range corrections
27	-[no]ionize	bool	no	Do a simulation including the effect of an X-Ray bombardment on your system

pdb2gmx – 4

Files

option	filename	type	description
-f	eiwit.pdb	Input	Structure file: gro g96 pdb tpr tpb tpa
-o	conf.gro	Output	Structure file: gro g96 pdb
-p	topol.top	Output	Topology file
-i	posre.itp	Output	Include file for topology
-n	clean.ndx	Output, Opt.	Index file
-q	clean.pdb	Output, Opt.	Structure file: gro g96 pdb

Other options

option	type	default	description
-[no]h	bool	no	Print help info and quit
-nice	int	0	Set the nicelevel
-[no]merge	bool	no	Merge chains into one molecule definition
-ff	string	select	Force field, interactive by default. Use -h for information.
-water	enum	spc	Water model to use: with GROMOS we recommend SPC, with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p or f3c
-[no]inter	bool	no	Set the next 8 options to interactive
-[no]ss	bool	no	Interactive SS bridge selection
-[no]ter	bool	no	Interactive termini selection, iso charged
-[no]lys	bool	no	Interactive Lysine selection, iso charged
-[no]arg	bool	no	Interactive Arganine selection, iso charged
-[no]asp	bool	no	Interactive Aspartic Acid selection, iso charged
-[no]glu	bool	no	Interactive Glutamic Acid selection, iso charged
-[no]gln	bool	no	Interactive Glutamine selection, iso neutral
-[no]his	bool	no	Interactive Histidine selection, iso checking H-bonds
-angle	real	135	Minimum hydrogen-donor-acceptor angle for a H-bond (degrees)
-dist	real	0.3	Maximum donor-acceptor distance for a H-bond (nm)
-[no]una	bool	no	Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine
-[no]ignh	bool	no	Ignore hydrogen atoms that are in the pdb file
-[no]missing	bool	no	Continue when atoms are missing, dangerous
-[no]v	bool	no	Be slightly more verbose in messages
-posrefc	real	1000	Force constant for position restraints
-vsite	enum	none	Convert atoms to virtual sites: none, hydrogens or aromatics
-[no]heavyh	bool	no	Make hydrogen atoms heavy
-[no]deuterate	bool	no	Change the mass of hydrogens to 2 amu

genbox – 4

Files

option	filename	type	description
-cp	protein.gro	Input, Opt.	Structure file: gro g96 pdb tpr tpb tpa
-cs	spc216.gro	Input, Opt., Lib.	Structure file: gro g96 pdb tpr tpb tpa
-ci	insert.gro	Input, Opt.	Structure file: gro g96 pdb tpr tpb tpa
-o	out.gro	Output	Structure file: gro g96 pdb
-p	topol.top	In/Out, Opt.	Topology file

Other options

option	type	default	description
-[no]h	bool	no	Print help info and quit
-nice	int	19	Set the nicelevel
-box	vector	0 0 0	box size
-nmol	int	0	no of extra molecules to insert
-try	int	10	try inserting -nmol*-try times
-seed	int	1997	random generator seed
-vdwd	real	0.105	default vdwaals distance
-shell	real	0	thickness of optional water layer around solute
-maxsol	int	0	maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored
-[no]vel	bool	no	keep velocities from input solute and solvent

grompp – 4

Files

option	filename	type	description
-f	grompp.mdp	Input, Opt.	grompp input file with MD parameters
-po	mdout.mdp	Output	grompp input file with MD parameters
-c	conf.gro	Input	Structure file: gro g96 pdb tpr tpb tpa
-r	conf.gro	Input, Opt.	Structure file: gro g96 pdb tpr tpb tpa
-rb	conf.gro	Input, Opt.	Structure file: gro g96 pdb tpr tpb tpa
-n	index.ndx	Input, Opt.	Index file
-p	topol.top	Input	Topology file
-pp	processed.top	Output, Opt.	Topology file
-o	topol.tpr	Output	Run input file: tpr tpb tpa
-t	traj.trr	Input, Opt.	Full precision trajectory: trr trj cpt
-e	ener.edr	Input, Opt.	Energy file: edr ene

Other options

option	type	default	description
-[no]h	bool	no	Print help info and quit
-nice	int	0	Set the nicelevel
-[no]v	bool	yes	Be loud and noisy
-time	real	-1	Take frame at or first after this time.
-[no]rmvsbds	bool	yes	Remove constant bonded interactions with virtual sites
-maxwarn	int	0	Number of allowed warnings during input processing
-[no]zero	bool	no	Set parameters for bonded interactions without defaults to zero instead of generating an error
-[no]renum	bool	yes	Renumber atomtypes and minimize number of atomtypes