On Thu, Oct 15, 2015 at 2:46 PM, Khabiri, Morteza <khabiri.med.umich.edu>
wrote:
> Dear Jason
> I have replied you in the morning. It did not sent to amber list since it
> contain jpg file (I think).
> I am doing MD in isotropic NVT ensemble. So, I dont have any slab
> geometry in my MD. The box size is qiute enough that the distance btw
> protein and the wall is bigger that the half of the box size.
> Regarding unwrap: I would say I mean the solution(water + ions) diffused
> out of the box while the box size is kept fixed.
>
> The same system as the one for ti calculations, was running before in NVT
> and iwrap=1 but in MD calculation and the wrap working well. All molecules
> kept in the simulation box and not diffuse out of the box. But, when I use
> the same syetem for ti calculation, the iwrap is not working anymore.
> Anyway, It should not effect the energy calculation but I am wondering why
> it is iwrap not working in ti calculation.
>
> Please let me know if the description is not clear.
>
It is much clearer now, thank you. Can you check the results of
`autoimage` from cpptraj on these TI trajectories? This will help show
whether the coordinates are printed out incorrectly, or if there is just a
problem with imaging when TI is active in pmemd.
It does indeed sound like some kind of bug. It's important to determine
whether it's a bug affecting just convenience or actual results, though.
Hopefully one of the developers responsible for the TI code will be able to
reproduce this behavior so they can work on fixing it.
Thanks for the report,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Oct 16 2015 - 05:00:02 PDT
