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Gromacs MD Flowchart

The document outlines the workflow for performing molecular dynamics simulations on multiple solvated molecules using GROMACS. It involves setting up the topology, generating the box coordinates, solvating the molecules, adding counter ions, generating input files for energy minimization, equilibration, and production simulations, and running the simulations. Key steps include using tools like pdb2gmx, genbox, genion, grompp, and mdrun.

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Vivek Sharma
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336 views2 pages

Gromacs MD Flowchart

The document outlines the workflow for performing molecular dynamics simulations on multiple solvated molecules using GROMACS. It involves setting up the topology, generating the box coordinates, solvating the molecules, adding counter ions, generating input files for energy minimization, equilibration, and production simulations, and running the simulations. Key steps include using tools like pdb2gmx, genbox, genion, grompp, and mdrun.

Uploaded by

Vivek Sharma
Copyright
© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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GROMACS Molecular Dynamics Simulations Flowchart For multiple molecules solvated in water Dallas Warren - 20/05/2005

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

Protein Databank File

.pdb

pdb2gmx
Topology File .top .gro Gromos File

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

editconf
Gromos File Topology File .gro
Adjust molecule numbers in .top file Adjust solvent and counter ion numbers in .top file

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

.top

genbox
Gromos File Topology File .gro .top

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

genbox
Gromos File Topology File Parameter File .gro .top .mdp

Generate Genion Input File


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

grompp
Binary Topology File .tpr

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

genion
Log File Gromos File Topology File Parameter File .log .gro .top .mdp

Generate MD Input File


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

grompp
Binary Topology File .tpr

GROMACS Molecular Dynamics Simulations Flowchart For multiple molecules solvated in water Dallas Warren - 10/02/2004

Binary Topology File

.tpr

MD for Energy Minimisation


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

mdrun
Trajectory File Log File Energy File Gromos File .trr .log .edr .gro .top .mdp

Generate MD Input File


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

Topology File Parameter File

grompp
Binary Topology File .tpr

MD PR for Water Equilibration


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

mdrun
Trajectory File Log File Energy File Gromos File Topology File Parameter File .trr .log .edr .gro .top .mdp

Generate MD Input File


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

grompp
Binary Topology File .tpr

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

mdrun
Trajectory File Log File Energy File Gromos File .trr .log .edr .gro

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