I am confused about setting the cell basis in NAMD. Initially, I set the cell basis according to my solvation box dimensions + 2 or 3A to separate the unit cells in the PBC. This is fine during the min and NVT equilibration steps since the volume is fixed but in the npt step, in the volume of my solvation box shrinks and lose about 15% of its initial volume to reach a high density around the solute. Should not we open the flexible cell option in NAMD to avoid the vacuum pockets in the solvation boxes and let the system adjust its cell basis according to the final volume ?
or I misunderstood the cell basis story ?
Use of a flexible cell means the pressure coupling is anisotropic. This is appropriate for crystalline systems, but not a normal solvated box where the solvent is homogeneous and therefore the pressure coupling should be applied isotropically. It is normal for a box to change size upon equilibration because most solvation protocols are simply approximations.
Use of a flexible cell means the pressure coupling is anisotropic. This is appropriate for crystalline systems, but not a normal solvated box where the solvent is homogeneous and therefore the pressure coupling should be applied isotropically. It is normal for a box to change size upon equilibration because most solvation protocols are simply approximations.
In addition to what Justin already pointed out, the use of a flexible cell in combination with "useconstantarea" is utilized to apply pressure only in the Z direction for systems containing surfaces or membranes.
The amount of water buffer included in your simulations depends on the electrostatic cutoff distance that you specify. The general idea behind a "dilute" simulation is that your solute will not interact with periodic images of itself. With a 12 A cutoff, you would need at least 6 A of water surrounding your solute; 8 A is a typical number that I used in my simulations of compact proteins. For complexes, you may need to adjust that number accordingly. There will be shrinkage of the volume once you begin enforcing constant pressure; this is inevitable. A 2-3 A water buffer does not do,I believe, anything useful.
Note: you may be dismayed by that fact that an 8 A water buffer means that you are mostly pushing water molecules around in your simulations. This is a consequence of performing NPT simulations. With today's cpu speeds, it is not as onerous as it was in the past. No one, to my knowledge, has mastered a transition from individual TIP3 water molecules to bulk dielectric. So, one just uses brute force (and advances in computational power) to build big water baths.
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