From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Apr 27 2018 - 20:17:10 CDT
If I understand your setup, you've simulated a globular protein in a minimal water box. Then I think you, loaded it up into VMD, did some RMSD-based analysis, and are wondering why your waterbox looks tilted. I think this is because your protein rotated during simulation to make better contacts with its periodic image. After protein alignment, it looks like the water box rotates rather than the protein. My recommendation is to increase your solvation box at a minimum. Right now, the protein is directly interacting with itself, since the minimal box only buys you 10 angstroms of distance between the closest protein parts across the periodic cell. In short, the simulation will need to be redone, since the simulation conditions aren't relevant to any sort of realistic condition.
On 2018-04-27 16:59:04-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
I ran ~12ns NPT equilibration of a spherical protein in a water box with 5A padding with NaCl and my simulation cell tilted during equilibration by about 5-8 degrees by the end of this run. The size of the box did not change and rmsd of the protein is about ~1.5A, the protein seems to be stable, i.e. not falling apart. The center of mass of the protein is at the origin and cell center is very close, within 0.5-1A on each axis. In the end of this run one of the residues partially sticks out of the box, but the structural integrity of that subunit is preserved.
What could be the reason for water box tilting? Can I still use this equilibrated structure for further calculations (such as ABF)?
Thanks in advance,
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