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)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> 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)
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Received on Tue Mar 08 2016 - 15:00:04 PST
