Alrighty, I'll give it a try and let you know, Thanks!
On Tue, Mar 8, 2016 at 3:38 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Yeah, give the AmberTools 15 version a try. If that seems to have the
> same behavior do me a favor and try the GitHub (beta) version:
> https://github.com/Amber-MD/cpptraj. That will give us a behavior
> baseline to work with. Thanks!
>
> -Dan
>
> On Tue, Mar 8, 2016 at 3:30 PM, Timothy Christopher Schutt
> <tschutt.mymail.mines.edu> wrote:
> > 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!
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > 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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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Mar 08 2016 - 15:00:05 PST
