Simulation box density decrease in NPT using position restraints

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1

Hi all,
Untill now i had studied many tutorials for md simulation in gromacs , in all tutorials people ise position restraints both in NVT and NPT run and then release in final production run.
I am doing md simulation of polymer plus ions (PEO+LiTFSI).
When i run NPT using position restraints for polymer my simulation box density decrease (it should increaseand reaches close to experimental) even after a long simulation run. When i don’t use position restraints it goes fine and reach close to experimental value.
My question is

  1. Is it necessary to run NPT with position restraints or we can go without it depending on our results.
  2. If it is necessary to use then what makes my system wrong when i use this
  3. How much this position restraints effects our simulation results.

Please answer as soon as possible. Waiting

2

If you’re initial density is off, position restraints will prevent the density and volume to fully relax, which I suppose is your case.

Personally I never use position restraints, but then I have not worked with delicate protein structures that require careful equilibration. But I don’t see why you would need position restraints at all for simulating a polymer which anyhow doesn’t start from an accurate (crystal) structure.