pdb2gmx

editconf

genbox

grompp

Protein Databank File .pdb

Topology File .top

Gromos File .gro

Gromos File .gro

Gromos File .gro

Topology File .top

Topology File .top

Parameter File .mdp

Binary Topology File .tpr

Set Up Topology

Generate Box

Solvate Molecules

Generate Genion Input File

-f input.pdb-o output.gro-p output.top(-heavyh)

-f input.gro-o output.gro-bt tric/cubic/….-box dimensions (nm)

-cp input.gro-cs blank-p input/output.top-o output.gro

-f input.mdp-c input.gro-p input.top-o output.tpr

Multiple Molecules-cp input.gro-ci input.gro-p input/output.top-o output.gro-nmol number-seed number

genbox

gromppBinary Topology File .tpr

Generate MD Input File

-f input.mdp-c input.gro-p input.top-o output.tpr

genionLog File .log

Gromos File .gro

-s input.tpr-o output.gro-g output.log-np/nn number-pname/nname name +ve/-ve-pq/nq charge-random-seed number

Counter Ions

Topology File .top

Parameter File .mdp

GROMACS Molecular Dynamics Simulations FlowchartFor multiple molecules solvated in water

Dallas Warren - 20/05/2005

Adj

ust s

olve

nt a

nd c

ount

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mbe

rs in

.top

file

Gromos File .gro

Topology File .top

Adj

ust m

olec

ule

num

bers

in .t

opfil

e

mdrunTrajectory File .trr

Log File .log

Energy File .edr

Gromos File .gro

grompp

Topology File .top

Parameter File .mdp

Binary Topology File .tpr

MD PR for Water Equilibration

Generate MD Input File

Binary Topology File .tpr

mdrunTrajectory File .trr

Log File .log

Energy File .edr

Gromos File .gro

MD Simulation

-s input.tpr-o output.trr-c output.gro-e energy.edr-g output.log-v <verbose>

-s input.tpr-o output.trr-c output.gro-e energy.edr-g output.log-v <verbose>

-f input.mdp-c input.gro-t input.trr-p input.top-o output.tpr-np number

grompp

Topology File .top

Parameter File .mdp

Generate MD Input File-f input.mdp-c input.gro-p input.top-o output.tpr

mdrunTrajectory File .trr

Log File .log

Energy File .edr

Gromos File .gro

-s input.tpr-o output.trr-c output.gro-e energy.edr-g output.log-v <verbose>

MD for Energy Minimisation

Binary Topology File .tpr

GROMACS Molecular Dynamics Simulations FlowchartFor multiple molecules solvated in water

Dallas Warren - 10/02/2004