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
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 04 2022 - 13:37:46 PDT
