Hi Dan,
I was using Amber14 with AmberTools15, simulations were run in NVE ensemble
with pmemd.cuda_SPFP. the cpptraj came with the originalinstall... soo
version AmberTools15?
-Timothy Schutt
CSM Dr. Maupin Research Group
On Tue, Mar 8, 2016 at 2:43 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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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>
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Received on Tue Mar 08 2016 - 15:00:03 PST
