On Wed, 2015-07-01 at 15:01 -0700, Naomi Rose Latorraca wrote:
> Hi Amber users,
>
> I've been using Amber software to run simulations of a small membrane
> protein embedded in a POPC bilayer. The system, which is parameterized
> with charmm parameters, is about 35,000 atoms in size and has
> dimensions of 70 x 70 x 73 angstroms.
>
> For pressure control settings, I've been using anisotropic coupling
> (npt=2) with the Monte Carlo barostat (barostat=2). However, on the
> time scale of tens to hundreds of nanoseconds, we observe lengthening
> of the system in a single lateral dimension. Upon visualizing the
> periodic box images in VMD, we see that boxes are shearing against
> each other in the lateral dimensions in the bilayer and that protein
> images are getting quite close to the edges of each individual box.
What program are you using? sander or pmemd/pmemd.cuda? And what
version are you using?
As Ross mentioned, the Monte Carlo barostat had sub-optimal move sets
for anisotropic and semi-isotropic pressure scaling (I had actually
thought the latter was disabled in pmemd 14 altogether). However, those
move sets have been improved since the release of Amber 14, and these
improvements should be in sander if you are using the latest AmberTools
15 release.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Jul 02 2015 - 06:00:02 PDT
