Hi Rama, Thanks for your quick reply.
Catenate two trajectory with help of trjcat -h to get snapshot of particular time use trjconv -dump <time> use appropriate pbc option I have also used trjconv with -dump and -pbc nojump options, but still I have same problem. you are using -b 10000 -e 10000 means the snapshot at 10 ns No, it is the snapshot at 20ns. (the confusion comes from the file names.) So I think conf20.gro is snapshot at 20 ns so they may differ ... With Best Wishes, Rama David I am so confused with this problem... Turgay
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