1. pdb2gmx_d -ignh -ff gromos43a1 -f tripeptide.pdb -o fws.pdb -p fws.top (choose water model: if want to do in vacume choose none) 2.

editconf_d -bt octahedron -f fws.pdb -o fws-b4sol.pdb -d 1.0 3. grompp_d v -f sd.mdp -c sd.gro -p fws.top -o sd.tpr -maxwarn 5 4. mdrun_d -v -deffnm sd see energy converged or not; if not go to code 5 followed by 6 several time , or run code in loop ( code 7) and if converged then go to 8 followed by 9 5. grompp_d -v -f sd.mdp -c sd.gro -p fws.top -o sd.tpr -maxwarn 5 6. mdrun_d -v -deffnm sd 7. for i in {1..10}; do grompp_d -v -f sd.mdp -c sd.gro -p fws.top -o sd.tpr -maxwarn 5;mdrun_d -v -deffnm sd ;rm \#*;done here rm \#* is for removing back off files 8. grompp_d -v -f cg.mdp -c sd.gro -p fws.top -o cg.tpr -maxwarn 5 9. mdrun_d -v -deffnm cg if not converged do 10 and 11 repeatidly of do 12; If converged go to 13 10. grompp_d -v -f cg.mdp -c cg.gro -p fws.top -o cg.tpr -maxwarn 5 11. mdrun_d -v -deffnm cg OR 12. for i in {1..10}; do grompp_d -v -f cg.mdp -c cg.gro -p fws.top -o cg.tpr -maxwarn 5;mdrun_d -v -deffnm cg ;rm \#*;done 13. grompp_d -v -f lbfgs.mdp -c cg.gro -p fws.top -o lbfgs.tpr -maxwarn 5 14. mdrun_d -v -deffnm lbfgs If not converged do 15 and 16 several times until it converge or go to 17

15. grompp_d -v -f lbfgs.mdp -c lbfgs.gro -p fws.top -o lbfgs.tpr -maxwarn 5 16. mdrun_d -v -deffnm lbfgs 17. for i in {1..10}; do grompp_d -v -f lbfgs.mdp -c lbfgs.gro -p fws.top -o lbfgs.tpr -maxwarn 5;mdrun_d -v -deffnm lbfgs ;rm \#*;done 18. 19. grompp_d -v -f nm.mdp -c lbfgs.gro -p fws.top -o nm.tpr -maxwarn 5 mdrun_d_mpi -v -s nm.tpr -mtx nm.mtx IF WANT RUN IN PARALLEL ( mpirun) CASE 1 : If want to run in any other node then where you are now; (i)first go to local node (ii) make machine file: vi machine ; then write compute-0-15; I.e computenodenumber(without space) then hit following code: (iii) mpirun -nolocal -machinefile machine mdrun_d_mpi -v -s nm.tpr -mtx nm.mtx

(iv) mpirun -nolocal machinefile machine g_nmeig_d_mpi -f nm.mtx -s nm.tpr -ol eigenvalue.xvg -v eigenvector.trr -of eigenfreq.xvg -last 10000 (v) mpirun -nolocal machinefile machine trjconv_d_mpi -f eigenvector.trr -s nm.tpr -o eigenvector.gro -last 1000000 ( -last 10000 is for showing 1000 values of eigenvalue) CASE 2; I you are in high memory node then all codes are same but in place just write mpirun instead of mpirun - nolocal -machinefile machine YOU DONE ( FINISHED NM ANALYSIS))) g_nmeig_d -f nm.mtx -s nm.tpr -ol eigenvalue.xvg -v eigenvector.trr -of eigenfreq.xvg

CONVERT FROM BINARY TO READABLE:: gmxdump -mtx nm.mtx

TO SEE SOME ALREADY USED Commands: !first word of command of half command ( there should not be space between ! And command word)

PDB FILE the pdb is http://www.rcsb.org/pdb/explore.do?structureId=1omb, you can download it and then upload it to torrey. But you can also use the 1omb.pdb in your directory, as we have tried, it is the same as the pdb in pdb bank At this time, please do not use wget... remember to give -ignh when pdb2gmx, or you will get errors.

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