Should I be surprised with very low RMSD for my membrane protein simulation ?

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Justin Lemkul Popular answer

Did you forget to turn off position restraints? That is an incredibly low RMSD.

Justin Lemkul

Roshan Shrestha

I indeed turn off the position restraint on my peptide by removing it from the topology file. But, I did an erroneous mistake of still using -DPOSRES in my npt.mdp file for production run, which when grommped produced a tpr file and mdout.mdp which I sent to my supervisor abroad who before running mdrun in his cluster removed -DPOSRES from the mdout.mdp. I am not sure if it still removed position restraint on the protein or not.

If there is a position restraint energy term in the .log or .edr, then restraints were applied. The value you have for RMSD corresponds to almost zero movement; I have never seen a protein that stable in the absence of restraints.

Yeah, there is indeed restraints applied like in this case:

DD step 18779999 vol min/aver 0.964 load imb.: force 0.7%

Step Time Lambda

18780000 37560.00000 0.00000

Energies (kJ/mol)

U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14

9.43764e+04 6.67466e+04 8.61750e+02 -1.89666e+02 1.11963e+04

Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.

-1.19845e+05 -4.78540e+03 -5.76670e+03 -7.17141e+05 2.24377e+03

Position Rest. Potential Kinetic En. Total Energy Temperature

2.60875e+02 -6.72043e+05 2.22631e+05 -4.49411e+05 3.09491e+02

Pres. DC (bar) Pressure (bar) Constr. rmsd

-1.16229e+02 -4.09937e+00 8.72254e-06

So, it seems I will have to run the simulation once again.