Well dang - I'll take another look at the code. Is this an orthogonal
box or non-orthogonal?
Thanks for the report.
-Dan
On Tue, Aug 9, 2022 at 6:59 AM Cianna Calia <ccalia.ucsd.edu> wrote:
>
> Update: I tried the diffusion function from cpptraj version 6.13.0 with a different test case, now with a longer trajectory (100 ns), and this time I see big differences between the data from before unwrapping vs. after unwrapping - bigger differences than I saw with the version I was using before (V4.25.6). See attached plot; this is comparing the "R" MSD datasets obtained using V6.13.0 with this input:
>
> parm ../../water_box.prmtop
> trajin ../../water_box_100ns_1.nc
> diffusion out one_waterO_diff_cpptraj_test_before_unwrappingbyatom.dat time 2.0 ":1.O" nocalc
> unwrap byatom
> diffusion out one_waterO_diff_cpptraj_test_after_unwrappingbyatom.dat time 2.0 noimage ":1.O" nocalc
>
> Maybe the updated diffusion function is introducing another issue?
>
> Thanks,
> Cianna
>
> On Sun, Jul 31, 2022 at 10:11 AM Cianna Calia <ccalia.ucsd.edu> wrote:
>>
>> I tried it with the same test case I'd been using before - now the MSD data comes out exactly the same before and after unwrapping.
>>
>> Thanks again,
>> Cianna
>>
>> On Sun, Jul 31, 2022 at 7:54 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>
>>> Hi,
>>>
>>> I've fixed the behavior (I think) as of GitHub version 6.13.0
>>> (https://urldefense.com/v3/__https://github.com/Amber-MD/cpptraj/pull/984__;!!Mih3wA!H_XyP0NIHpChvZKV0aeMYpqJniRDBIwzKlnh1jiLbVQkUCfMFUV0bY2uCxtsvE7AU-OR9GqldO8949WK-Tr9$ ).
>>>
>>> Let me know if you get a chance to try it out.
>>>
>>> -Dan
>>>
>>> On Fri, Jul 29, 2022 at 7:57 PM Cianna Calia <ccalia.ucsd.edu> wrote:
>>> >
>>> > Interesting, thanks. Right, the diffusion constants are pretty close; I had just been looking at these numbers since it's specifically the MSD that I needed for something.
>>> >
>>> > Thanks so much for the explanation; that helps a lot. Enjoy your vacation.
>>> >
>>> > Cianna
>>> >
>>> >
>>> >
>>> > On Fri, Jul 29, 2022 at 4:20 PM Daniel Roe via AMBER <amber.ambermd.org> wrote:
>>> >>
>>> >> Yeah, I'm pretty sure I know what's going on here. The TL;DR
>>> >> explanation is that the current way I correct for imaging in diffusion
>>> >> will gradually diverge from the way 'unwrap' corrects for imaging.
>>> >> Neither is wrong per se, they just have different strategies to
>>> >> correct for imaging. Arguably the 'unwrap' way is more "correct"
>>> >> because it's not using a summation under the hood. You showed the raw
>>> >> numbers but I'm guessing the diffusion constants calculated from those
>>> >> files are probably really close right?
>>> >>
>>> >> Anyway, the fix (to make 'diffusion' correct imaging the way 'unwrap'
>>> >> does) is simple but will require some testing on my part, and I'm
>>> >> about to head out on vacation. Once I'm back I'll get the fix in, but
>>> >> until then your best bet is probably to "unwrap" first and then
>>> >> calculate diffusion.
>>> >>
>>> >> Thanks for the report.
>>> >>
>>> >> -Dan
>>> >>
>>> >> On Fri, Jul 29, 2022 at 6:56 PM Cianna Calia <ccalia.ucsd.edu> wrote:
>>> >> >
>>> >> > I'm using an orthorhombic box (roughly cubic since I'd used "iso" with solvatebox in tleap).
>>> >> > cpptraj with AmberTools20
>>> >> > pytraj version 2.0.5
>>> >> >
>>> >> > When I compare cpptraj's MSD data before vs. after unwrapping with byatom, the differences are ones to tens of Å^2. The maximum differences in x, y, z, and r datasets are:
>>> >> >
>>> >> > max X err: 7.819200000000137
>>> >> > max Y err: 13.486300000000028
>>> >> > max Z err: 18.626699999999914
>>> >> > max R err: 24.975800000000163
>>> >> >
>>> >> > It's off by more than tenths or hundredths.
>>> >> >
>>> >> > Tailing the two cpptraj data files shows the difference - End of the datafile from before unwrapping:
>>> >> >
>>> >> > 1995 2774.8698 1317.9164 699.3513 757.6022 52.6770
>>> >> > 1996 2590.9952 1182.8005 617.1339 791.0609 50.9018
>>> >> > 1997 2672.6255 1248.8877 684.0725 739.6653 51.6974
>>> >> > 1998 2666.3472 1224.3471 674.2470 767.7531 51.6367
>>> >> > 1999 2700.3229 1240.0459 721.4465 738.8306 51.9646
>>> >> >
>>> >> > End of the datafile from after unwrapping:
>>> >> >
>>> >> > 1995 2785.2869 1312.0513 705.1366 768.0990 52.7758
>>> >> > 1996 2602.1418 1177.2445 622.5693 802.3280 51.0112
>>> >> > 1997 2684.3411 1243.1784 689.7944 751.3682 51.8106
>>> >> > 1998 2677.9833 1218.6942 679.9278 779.3613 51.7492
>>> >> > 1999 2714.8978 1234.3569 727.3224 753.2185 52.1047
>>> >> >
>>> >> > Thanks for giving this your attention,
>>> >> > Cianna
>>> >> >
>>> >> >
>>> >> > On Fri, Jul 29, 2022 at 12:51 PM Daniel Roe via AMBER <amber.ambermd.org> wrote:
>>> >> >>
>>> >> >> Just one more question - just how different are the results? Are they
>>> >> >> pretty close (within a few tenths/hundreths of an Ang.) or are they
>>> >> >> way off?
>>> >> >>
>>> >> >> -Dan
>>> >> >>
>>> >> >> On Fri, Jul 29, 2022 at 3:49 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>> >> >> >
>>> >> >> > Hi,
>>> >> >> >
>>> >> >> > I think I see the behavior you are seeing. I need to look into it more
>>> >> >> > and I'll update you with what I find.
>>> >> >> >
>>> >> >> > What kind of unit cell are you using? Also, what versions of cpptraj
>>> >> >> > and pytraj are you using?
>>> >> >> >
>>> >> >> > Thanks!
>>> >> >> >
>>> >> >> > -Dan
>>> >> >> >
>>> >> >> > On Mon, Jul 25, 2022 at 8:58 AM Cianna Calia via AMBER
>>> >> >> > <amber.ambermd.org> wrote:
>>> >> >> > >
>>> >> >> > > Hello AMBER community!
>>> >> >> > >
>>> >> >> > > I am wondering if anyone can help me understand how the diffusion functions
>>> >> >> > > in pytraj/cpptraj handle unwrapping. When I try using pytraj to calculate
>>> >> >> > > an atom's MSD from a trajectory unwrapped in cpptraj (with "unwrap
>>> >> >> > > byatom"), I am unsure why it deviates from pytraj's result for the original
>>> >> >> > > wrapped trajectory, since I thought pytraj would deal with unwrapping
>>> >> >> > > automatically in a way that would give the same result as using the already
>>> >> >> > > unwrapped trajectory. But the X, Y, and Z datasets differ starting where
>>> >> >> > > unwrapping becomes relevant for each dimension.
>>> >> >> > >
>>> >> >> > > More detail - I have the original wrapped trajectory
>>> >> >> > > 1hg7_WT_cubic_100ns_1_last2ns.nc and an unwrapped trajectory
>>> >> >> > > unwrap_2ns_test1.nc made in cpptraj like this:
>>> >> >> > >
>>> >> >> > > parm 1hg7_WT_cubic.prmtop
>>> >> >> > > trajin 1hg7_WT_cubic_100ns_1_last2ns.nc
>>> >> >> > > unwrap byatom
>>> >> >> > > trajout unwrap_2ns_test1.nc
>>> >> >> > >
>>> >> >> > > I tried the following diffusion calculations with pytraj:
>>> >> >> > >
>>> >> >> > > import pytraj as pt
>>> >> >> > >
>>> >> >> > > original_traj = pt.load('1hg7_WT_cubic_100ns_1_last2ns.nc',
>>> >> >> > > '1hg7_WT_cubic.prmtop')
>>> >> >> > > pt_diffusion_orig_traj = pt.diffusion(original_traj, '.1730', dtype='dict',
>>> >> >> > > frame_indices=[i for i in range(len(original_traj))])
>>> >> >> > >
>>> >> >> > > unwrapped_traj = pt.load('unwrap_2ns_test1.nc', '1hg7_WT_cubic.prmtop')
>>> >> >> > > pt_diffusion_unw_traj = pt.diffusion(unwrapped_traj, '.1730', dtype='dict',
>>> >> >> > > frame_indices=[i for i in range(len(unwrapped_traj))])
>>> >> >> > >
>>> >> >> > > I am hoping for clarification on why pt_diffusion_orig_traj and
>>> >> >> > > pt_diffusion_unw_traj are not the same.
>>> >> >> > >
>>> >> >> > > I observe the same situation when I do analogous calculations with cpptraj
>>> >> >> > > as opposed to pytraj. I also tried seeing how the noimage option with the
>>> >> >> > > cpptraj diffusion function affects the results, and I am similarly confused
>>> >> >> > > about why the two diffusion calculations below give different results
>>> >> >> > > (again, differing starting from where there's unwrapping):
>>> >> >> > >
>>> >> >> > > parm 1hg7_WT_cubic.prmtop
>>> >> >> > > trajin 1hg7_WT_cubic_100ns_1_last2ns.nc
>>> >> >> > > diffusion out orig_traj_1730_diff_cpptraj.dat time 1.0 "@1730" nocalc
>>> >> >> > > unwrap byatom
>>> >> >> > > diffusion out unwrapped_traj_1730_diff_cpptraj.dat time 1.0 noimage "@1730"
>>> >> >> > > nocalc
>>> >> >> > >
>>> >> >> > > Taking out the "byatom" option makes no noticeable difference, nor does
>>> >> >> > > removing the "noimage" option from the diffusion command acting on the
>>> >> >> > > already unwrapped trajectory. The difference between the diffusion data
>>> >> >> > > before and after unwrapping here is not the same as the difference I
>>> >> >> > > observe when I use the diffusion command on the original wrapped trajectory
>>> >> >> > > with vs. without the "noimage" option.
>>> >> >> > >
>>> >> >> > > Thanks in advance for any help with understanding this!
>>> >> >> > > Cianna Calia
>>> >> >> > > _______________________________________________
>>> >> >> > > AMBER mailing list
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>>> >> >>
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Received on Tue Aug 09 2022 - 07:30:02 PDT
