[gmx-users] RMSD of energy minimized structure

Seera Suryanarayana palusoori at gmail.com
Fri Sep 30 07:33:09 CEST 2016

Dear gromacs users,

I have done energy minimization of clustered PDBs. When I try to
calculate the RMSD between the minimized clustered PDB and the
starting structure of MD simulations I got the following warning.

If there are molecules in the input tarjectory file that are broken
across periodic boundaries, they cannot be made whole (or treadted as
whole) without you providing a run input file.

I did not get what does it mean. I have not get any output for RMSD.
Where I did wrong? Kindly tell me.

Thanks in advance
Graduate student

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