[gmx-users] RMSD values consideration

[SHYANTANI MAITI]

Dear all,
After using this command for computation of rmsd of backbone of protein
protein complex consisting of three proteins :
/home/locuz/apps/gromacs/5.1/bin/gmx_mpi rms -f md_0_1.trr -s md_0_1.tpr
The rmsd is drastically increasing from 1 to 6 nm and after that it again
decreases to 1nm. can I use this result for my analysis? Is the rmsd
correctly obtained?
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Best regards,
*Shyantani Maiti*