[gmx-users] RMSD plot

tarak karmakar tarak20489 at gmail.com
Sun Jul 29 19:39:54 CEST 2012

Dear All,

In my initial protein pdb structure I have added some external ligand
molecules and as a result of that there are several short contacts.
So, well, I minimized the system and then got the 'prot_min.gro' file.
Now after the equilibration run, I plotted the RMSD of the resulting
trajectory with respect to the initial pdb structure. So as the pdb
had some short contacts, the resulting RMSD is showing large
increasing value around 0.4-0.5 nm.

1) Then, is it better to plot [ for reporting purpose ] the RMSD of
the trajectory with respect to the minimized coordinate file rather
than w. r. t. the initial PDB file?
2) What is the acceptable range of RMSD for a protein simulation ? (
below 0.2 nm !! )


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