From: P.-L. Chau (pc104_at_pasteur.fr)
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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