[gmx-users] RMSD values consideration

Ahmed Mashaly mashaly_1988 at yahoo.com
Wed Mar 28 09:15:50 CEST 2018

Try using trjconv to remove pbc before analysis
  On Wed, 28 Mar, 2018 at 8:43 am, SHYANTANI MAITI<shyantani.maiti at gmail.com> wrote:   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?
Best regards,
*Shyantani Maiti*
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