sorry the mail was not complete and accidentally sent i m sending it again
Hi 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 (38-60 ns) 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 full.tpr -f total.xtc -o gyrate.xvg My question is can we use the starting tpr file (full.tpr) along with the merged trajectory file (total.xtc) to do some analysis like for example radius of gyration. because when i am using g_gyrate -s full_part5.tpr -f full_part5.xtc -o gyrate_part5.xvg i am getting a different result. same way if i am using pbc nojump option for converting the trajectories using different tpr file i am getting different results trjconv -s full.tpr -f total.xtc -o nojump.xtc -pbc nojump g_gyrate -s full.tpr -f nojump.xtc -o gyrate.xvg and then trjconv -s full_part5.tpr -f full_part5.xtc -o part5_nojump.xtc -pbc nojump g_gyrate -s full_part5.tpr -f part5_nojump.xtc -o gyrate_part5.xvg so ideally the part 5 (38 - 60 ns) should be identical in both the graphs but it not true, both graphs remarkably different. Is there any possiblity to merge tpr files of all the breaks and then use that for merged trajectory. I don't know how to deal with that. please help me. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
