From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Fri Apr 27 2018 - 20:31:52 CDT
Indeed, in my previous simulations I have used more padding and have not
seen this effect. Thank you for pointing it out, it slipped my mind!
On Fri, Apr 27, 2018 at 9:17 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
> Hi Olga,
> 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:
> Hi all,
> 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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