Re: lengthening time-step with constraints causes RMSD "jump"

From: P.-L. Chau (
Date: Thu Jun 02 2011 - 16:03:53 CDT

Thank you for your message.

> If your restraints are so strong that you require a .2 fs timestep then
> they are more rigid than a covalent bond. Why would you care that the
> protein is not fixed if it can only move .1 A?

I tried relaxing the constraints but I also got an RMSD "jump". I was
going to sort this query out first before going to the other one, but I
presume I might as well report this now.

I reduced the constraint strength by 1/4, but I see a "jump" in the RMSD.
The average value around which the RMSD fluctuated increased.

> Is your BOUNDARY energy the same before and after restart?

No, it increased enormously. Initially it was 16992 and at the end of the
100000-step simulation it was 1.53E7.

Could I ask you what the boundary energy signifies in general, please?
Many thanks!

> The other possibility I can think of is that there is something wrong
> with your structure that requires these small timesteps, not the
> restraints.

I see. The structure is obtained from the PDB, and I have only built a
hydrated membrane around it whilst keeping all protein atoms frozen.

> Are you using constant pressure at this point? That could also cause
> problems as the cell size fluctuates and rescaling the atom coordinates
> jerks them around their restraint points.

Yes, I used an NPT ensemble with the following specifications, where the
temperature was set at 10K:

  # Constant Temperature Control
  langevin on
  langevinDamping 1
  langevinTemp $temperature

  # Constant Pressure Control (variable volume)
  if {1} {
  useGroupPressure yes
  useFlexibleCell yes
  useConstantRatio yes

  langevinPiston on
  langevinPistonTarget 1.01325
  langevinPistonPeriod 200.
  langevinPistonDecay 50.
  langevinPistonTemp $temperature

It appears from what you wrote that I should at least reduce the
constraints so that the protein can move more. Are there any other things
I should try, too, please?

I am sorry to have bothered you again, and I thank you very much for your
kind advice and help!

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