Awesome! And do the calculated diffusion constants make sense? In my tests
v6.14.0 seemed to give results that made sense for the water models I
looked at (whereas 6.13.0 results looked too small).
-Dan
On Mon, Aug 15, 2022 at 12:33 PM Cianna Calia <ccalia.ucsd.edu> wrote:
> Hi - Just want to let you know, I've tested out V6.14.0's diffusion
> function some more with my 100 ns 9620 water trajectory and so far it seems
> to be working great: The data from before and after unwrapping comes out
> the same in every case I've tried.
>
> Thanks,
> Cianna
>
> On Wed, Aug 10, 2022 at 1:18 PM Cianna Calia <ccalia.ucsd.edu> wrote:
>
>> Awesome! I'll let you know if anything seems odd. Thanks so much!
>>
>> Cianna
>>
>> On Wed, Aug 10, 2022 at 1:06 PM Daniel Roe <daniel.r.roe.gmail.com>
>> wrote:
>>
>>> OK - this time I really really think I've got it fixed.
>>>
>>>
>>> https://urldefense.com/v3/__https://github.com/Amber-MD/cpptraj/pull/985__;!!Mih3wA!AL4lcpBl6-cpGdXYXwTPlsQ-4vXQRzabRDunoe35K8ZxVfZ525mETRGgpwU607du5wT2QRylKUYQe-Szpn97$
>>>
>>>
>>> Version is 6.14.0 - please beat it up as much as you can. I've tested
>>> with my own files and the files you sent me and everything looks like
>>> it makes sense now, but I've thought that before...
>>>
>>> As a bonus, I've now openmp-parallelized the diffusion and unwrap
>>> calcs (cpptraj.OMP), and sped up the unwrap calc by just over 2x by
>>> only calculating the unwrap vector when the entity in question has
>>> traveled more than half the box length in any dimension. The unwrap
>>> results are consistent with previous cpptraj results as far as I can
>>> tell, but again tell me if you see anything weird.
>>>
>>> Thanks again for reporting this!
>>>
>>> -Dan
>>>
>>> On Tue, Aug 9, 2022 at 7:08 PM Cianna Calia <ccalia.ucsd.edu> wrote:
>>> >
>>> > Ah, yeah I just thought of that - The traj I sent you has frames
>>> spaced far apart just because I was trying to make the file size smaller
>>> for easy sending and I forgot that this might create a different issue,
>>> oops. The original 100 ns traj I was testing this on had frames saved every
>>> 2 ps. In the meantime I'll see if I can find a segment of my traj that
>>> shows the problem but is short enough that I can send it with the full
>>> density of frames without the file being extremely big. Sorry about that.
>>> >
>>> > Thanks,
>>> > Cianna
>>> >
>>> > On Tue, Aug 9, 2022 at 3:42 PM Daniel Roe <daniel.r.roe.gmail.com>
>>> wrote:
>>> >>
>>> >> Hi,
>>> >>
>>> >> Thanks for the files!
>>> >>
>>> >> So one difference I see right off the bat is that in your test
>>> >> trajectory you're saving frames every 400 ps while in my test
>>> >> trajectories I was saving frames every 0.5-10 ps at most. I will look
>>> >> in more detail tomorrow but it's possible the imaging code in the
>>> >> "diffusion" action (which is a bit simpler than the code in the
>>> >> "unwrap" action) is getting confused by the much larger distance jumps
>>> >> in-between frames (due to the lower frequency at which the trajectory
>>> >> is being written). I'll dig into this more tomorrow.
>>> >>
>>> >> -Dan
>>> >>
>>> >> On Tue, Aug 9, 2022 at 3:58 PM Cianna Calia <ccalia.ucsd.edu> wrote:
>>> >> >
>>> >> > I tried V6.13.0 by doing the following:
>>> >> > git clone
>>> https://urldefense.com/v3/__https://github.com/Amber-MD/cpptraj.git__;!!Mih3wA!EGutLqXWJ4wRIIkndG8fvlbQIUef5NXczKaxgob--QNevHQ_mc81T-7rtD3pIXtkRUgL3BAZUhQHf3_Fdy5M$
>>> >> > Inside the cpptraj folder:
>>> >> > ./configure gnu
>>> >> > make install
>>> >> >
>>> >> > On Tue, Aug 9, 2022 at 12:44 PM Daniel Roe <daniel.r.roe.gmail.com>
>>> wrote:
>>> >> >>
>>> >> >> On Tue, Aug 9, 2022 at 3:15 PM Cianna Calia <ccalia.ucsd.edu>
>>> wrote:
>>> >> >> >
>>> >> >> > Do diff.1.dat and diff.2.dat come out the same for you?
>>> >> >>
>>> >> >> Yes, they're identical except for the header:
>>> >> >>
>>> >> >> $ diff diff.1.dat diff.2.dat
>>> >> >> 1c1
>>> >> >> < #Time D1[R] D1[X] D1[Y]
>>> D1[Z] D1[A]
>>> >> >> ---
>>> >> >> > #Time D2[R] D2[X] D2[Y]
>>> D2[Z] D2[A]
>>> >> >>
>>> >> >> > My current test system has 9620 waters; the 100 ns trajectory is
>>> > 23 GB which makes attaching it a little hard. Let me see if I can
>>> reproduce the issue using a shorter, sparser version of my traj and if I
>>> can then I will share that.
>>> >> >>
>>> >> >> Understood, thanks! I can also look into trying to make my traj
>>> >> >> available to you to try. How was your cpptraj compiled?
>>> >> >>
>>> >> >> -Dan
>>>
>>
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Received on Tue Aug 16 2022 - 05:00:03 PDT
