I have been running protein simulations using explicit water and have been using the stepwise minimization (water first followed by solute) and then heating (NVT) followed by density equilibration (NPT). I am using a similar protocol where protein is embedded 10 A above the GOLD surface. Water is added on both sides of surface.
We tried running a short 200 ps NVT run with Gold and protein atoms fixed (force constant of 2 kcal/mol A^2) however, upon visualization in VMD, we notice holes/bubbles (on the edges of the box). One would expect very little change in box dimension during NVT (holding atoms fixed). Is it an artifact of applying restraints or something is wrong with solvation protocol? We want to perform simulation where GOLD surface is always fixed. I will appreciate feedback.
Voids form during NVT because there is accessible volume within the unit cell and waters diffuse into it; the box in NVT is fixed (by definition) so you see the emergence of voids. A short NPT equilibration will solve it because the box will compress to eliminate the void space.
Voids form during NVT because there is accessible volume within the unit cell and waters diffuse into it; the box in NVT is fixed (by definition) so you see the emergence of voids. A short NPT equilibration will solve it because the box will compress to eliminate the void space.
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