http://manual.gromacs.org/online/getting_started.html

http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water

module load gromacs/5.0/INTEL-140-MVAPICH2-2.0

1) generate Gromacs-compatible coordinate and Topology Files

pdb2gmx -f 1UBQ.pdb -o protein.gro -p topol.top -ignh -v

2) editconf: rotate, translate coordinate file, define box size.
editconf -f protein.gro -o protein_box.gro -bt triclinic -d 0.5 -c  	//rectangular box
editconf -f protein.gro -o protein_box.gro -bt dodecahedron -d 0.5 -c   // sphere 

3) solvate the water box
gmx solvate -cp protein_box.gro -cs spc216.gro -o protein_sol.gro -p topol.top

4) Generate the topology and index files:
pdb2gmx -v -f protein_sol.gro -o protein_sol_final.gro -p topol_final.top -n protein_sol.ndx

5) Run pre-processor to set up MD run --> .tpr
combine the molecular structure (.gro file), topology (.top file) MD-parameters (.mdp file) -->
grompp -v -f 1UBQ.mdp -c protein_sol_final.gro -p topol_final.top -o 1UBQ_run

6) Run molecular dynamics simulation
mdrun -v -s 1UBQ_run.tpr -x -deffnm 1UBQ_output 

parallel run
mpirun -np 20 mdrun -s 1UBQ_run.tpr -x -deffnm output 
or
mpirun -np 20 mdrun_mpi_d -s 1UBQ_run.tpr -x -deffnm output

7)Analysis:
g_energy -f 1UBQ_output.edr -o energy.xvg
vmd 1UBQ_output.gro

.top: topology file contains a complete description of all the interactions in your peptide or protein. 
.gro: molecular structure (coordinates) in Gromos87 format, can be used as trajectory file
.mdp: Molecular Dynamics Parameter (.mdp) file contains all information about simulation itself e.g. time-step, number of steps, temperature, pressure etc.  -->mdout.mdp as output
.tpr: infor to run simulations
.xtc: trajectory file
.trr: trajectory file
.edr: energy file 
