[gmx-users] Re:continuation of run

alkasrivastava at iitb.ac.in alkasrivastava at iitb.ac.in
Fri Jul 25 12:25:14 CEST 2008


I am running a simulation for 60 ns but due to power cutt it stopped at
different time intervals and i continued the run with following command

1. tpbconv -s full.tpr -f full.trr -e full.edr -o full_part1.tpr -until 60000

2. nohup mpirun -np 2 mdrun_mpi -v -s full_part1.tpr -e full_part1.edr -c
after_full.gro -o full_part1.trr -x full_part1.xtc -g full_part1.log -nice
19 >& full_part1.job&

In a way i continued till 60 ns in 5 such breaks so now i have

full.tpr full.xtc
full_part1.tpr full_part1.xtc
full_part2.tpr full_part2.xtc
full_part3.tpr full_part3.xtc
full_part4.tpr full_part4.xtc
full_part5.tpr full_part5.xtc

Finally i merged all the trajectories using command

trjcat -f   full.xtc full_part1.xtc full_part2.xtc full_part3.xtc
full_part4.xtc full_part5.xtc -o total.xtc

Now for the calculation of radius of gyration the command i have used

g_gyrate -s fu

More information about the gromacs.org_gmx-users mailing list