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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
er io
n nu
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