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