Hi,
What version of cpptraj are you using?
-Dan
On Tue, Mar 8, 2016 at 2:11 PM, Timothy Christopher Schutt
<tschutt.mymail.mines.edu> wrote:
> Dear amber experts and users,
>
> I think I've discovered a bug in cpptraj that we should be aware of (Or
> else I'm doing something wrong).
>
> I have been troubleshooting some odd behavior from the cpptraj diffusion
> output data - there would be large jumps in the MSD randomly, especially
> accentuated by larger and more viscous solvent molecules (like ionic
> liquids). The first thought was of course box-boundary error trying to
> unwrap the periodic boundary. I dismissed this after verifying that when
> molecules crossed one boundary the MSD remained intact. Later on I came
> back to that thoery though and isolated that the problem is when one
> molecule sitting on the box edge or corner happens to cross the boundary in
> two different dimensions during the same frame change. In this scenario the
> wrapping of the second periodic boundary is not accounted for and the MSD
> jumps up by n * L^2/N (L= simulation box length. n= number of molecules in
> the mask double wrapping that frame, and N = the number of molecules in the
> mask). Although in large water-solvated systems there's enough molecules
> and a small enough surface area/volume ratio that these jumps aren't
> readily noticed they do still artificially increase the simulated diffusion
> rates output by cpptraj.
>
> Am I doing something wrong or is this a persistent problem throughout
> cpptraj calculations? Is there a patch/fix for this? For the moment I'm
> just using the *_x and *_y diffusion data because in my system there should
> be no dimensional bias and it seems the z contains the vast majority of the
> errors (presumably because the first wrap-around is accounted for
> accurately leaving most often the z to receive the error).
>
> This is my current theory anyway. Has anyone else observed this behavior?
> Is there a better fix than just using X and Y and assuming symmetry?
>
> Thanks!
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Mar 08 2016 - 14:00:04 PST
