Useful commands for Gromacs Post MD Analysis

############TO CHECK THE TRJ##############################

gmx_mpi check -f md_0_1.xtc

##########################################################

############POST-PROCESSING##########################################

gmx_mpi trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact -center

##############ANALYSIS########################################################\<<<<<RMSD>>>>>>

gmx_mpi rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns

<<<<<RMSF>>>>>>

gmx_mpi rmsf -f md_0_1_noPBC.xtc -s md_0_1.tpr -o rmsf.xvg -res

<<<<<HBOND>>>>>>

gmx_mpi hbond -f md_0_1_noPBC.xtc -s md_0_1.tpr -num hbond_L+M.xvg

<<<<<Rg>>>>>>

gmx_mpi gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg

##############TO SAVE SPECIFIC TIME FRAME SNAPSHOT IN PDB##############

gmx_mpi trjconv -s md_0_1.tpr -f md_0_1_noPBC.xtc -o 10ns.pdb -pbc mol -ur compact -dump 10000

gmx_mpi trjconv -s md_0_1.tpr -f md_0_1_noPBC.xtc -o 87ns.pdb -pbc mol -ur compact -dump 8000

gmx_mpi trjconv -s md_0_1.tpr -f md_0_1_noPBC.xtc -o 10ns.pdb -pbc mol -ur compact -dump 10000

gmx_mpi trjconv -s md_0_1.tpr -f md_0_1_noPBC.xtc -o 1ns.pdb -pbc mol -ur compact -dump 1000

gmx_mpi trjconv -s md_0_1.tpr -f md_0_1_noPBC.xtc -o 2ns.pdb -pbc mol -ur compact -dump 2000

<<<<<EXTRACT PARTICULAR FRAMES IN BETWEEN>>>>>>

gmx_mpi trjconv -s md_0_1.tpr -f md_0_1_noPBC.xtc -o md_0_1_noPBC1-40ns.xtc -pbc mol -ur compact -b 10000 -e 40000 -dt 100

<<<<<TO CHANGE NO. OF FRAMES>>>>>>

gmx_mpi trjconv -s md_0_1.tpr -f md_0_1_noPBC20-50ns.xtc -o md_0_1_noPBC20-50ns_10000.xtc -pbc mol -ur compact -dt 10000

cluster .xtc

gmx_mpi cluster -f md_0_2_noPBC.xtc -s md_0_2.tpr

gmx_mpi cluster -f md_0_1_noPBC.xtc -s md_0_1.tpr -sz 5

gmx_mpi cluster -f md_0_1_noPBC.xtc -s md_0_1.tpr -sz 5

make index file

gmx make_ndx -f em.gro -o index.ndx

Further Analysis of trajectory (follow link)

http://nmr.chem.uu.nl/~adrien/course/molmod/analysis1.html