Very High RMSD Value from NAMD Simulation

From: Efthymiou, Christos (
Date: Wed May 11 2022 - 14:19:37 CDT


I am using QwikMD/NAMD to prepare the molecular dynamics simulation files to run a simulation on a supercomputer. The system I am simulating contains two protein chains that bind to one another.

I would like to recreate the simulation conditions found in a paper shown here:

"For each site of interaction on X with Y, three explicit solvent MD simulations were performed using NAMD and the CHARMM27 force field. Structures were initially minimized with the water molecules contained in the crystallographic structure and subsequently solvated in a cubic TIP3P water box leaving a minimum margin of 12 Ĺ around the protein structure. Sodium and chloride ions were also added to the water box, bringing the ionic strength to 150 mM. Minimization of the solvated structure was performed for 25,000 steps (50 ps) before heating to 310 K over 64 ps. Next, equilibration was performed where all protein atoms were constrained at 10 kcal/mol/Ĺ2 initially and then relaxed to 5, 2, and 1 kcal/mol/Ĺ2 before removing constraints altogether for the final equilibration run. Following equilibration, the MD simulation was run with periodic boundary conditions, Langevin temperature and pressure control, and particle mesh Ewald (PME) electrostatics. Relevant parameters for the simulation included a nonbonded interaction cutoff of 12 Ĺ and a switching distance of 10 Ĺ. Hydrogen bonds were held constant according to the SHAKE algorithm as an integration time step of 2 fs was used."

To recreate the above, I used QwikMD with the following Protocol:

  * Minimization - 25000 steps, backbone restraint, NpT, 0 Temp, 1 Pressure
  * Annealing - 35000 steps, backbone restraint, NpT, 37 Temp, 1 Pressure
  * Equilibration - 50000 steps, protein restraint, NpT, 37 Temp, 1 Pressure
  * Equilibration.1 - 50000 steps, protein restraint, NpT, 37 Temp, 1 Pressure
  * Equilibration.2 - 50000 steps, protein restraint, NpT, 37 Temp, 1 Pressure
  * Equilibration.3 - 50000 steps, protein restraint, NpT, 37 Temp, 1 Pressure
  * Equilibration.4 - 50000 steps, no restraint, NpT, 37 Temp, 1 Pressure
  * MD - 500000 steps, no restraint, NpT, 37 Temp, 1 Pressure

I then edited the .conf files with Notepad++ for the equilibration steps to make constraintscaling 10 for Equilibration.conf, constraintscaling 5 for Equilibration.1.conf, etc. to mimic the 10 kcal/mol/Ĺ2, 5, 2, etc. constraints from the paper above. Is this the best way to do this? Or is there another way? Additionally, I am not sure how to hold the Hydrogen bonds constant according to the SHAKE algorithm or if this is done automatically.

I then transfer the files to the supercomputer and run the simulation before transferring it back to my computer for analysis. When I plot the RMSD for the MD trajectory, I see a very large RSMD value. It jumps from around 0 angstroms to nearly 5 angstroms within the first couple hundred picoseconds, and continues increasing to over 15 angstroms over the course of the 10 ns simulation.

Are there any reasons why the RMSD value is so high? I have tried searching online for reasons why an RMSD value would be so high during a simulation, and I cannot find any information. I am not sure if I am not properly recreating the conditions from the paper above or what parameters I can try manipulating to make the RMSD value more reasonable. In the paper, the RMSD stayed under 5 angstroms so I am confused as to why my RMSD values are so high. I have also tried it several times and the same thing happens each time.

I appreciate any help!

This archive was generated by hypermail 2.1.6 : Tue Dec 13 2022 - 14:32:44 CST