Thank you Dan,
I will install, check and let you know.
It's nice to have a command for autoimage for trajectories wrapped byatom.
I also tried to do image using approach I was trying to explain. And it
worked, but your approach is better and straightforward.
Thank you again.
-Shailesh
On Jun 28, 2017 2:46 PM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> It turns out there wasn't a bug here, but I did have to create a new
> command: 'fiximagedbonds' (details below). The new command is
> available in the GitHub version of cpptraj:
> (https://github.com/Amber-MD/cpptraj).
>
> The 'unwrap' command relies on having a reference structure that is
> not too different from the frames you want to unwrap. Based on the
> files you gave me you can see that in the first frame of the
> trajectory the protein (residues 1 to 286) appears to be rotated about
> 90 degrees with respect to the reference. Therefore it appears that
> the atoms travel huge distances from the reference to the first frame
> and 'unwrap' can't make heads or tails of it. It's particularly
> problematic since imaging was done by atom, so you end up "breaking"
> bonds. The 'fiximagedbonds' command will restore structures that have
> been imaged this way. Basic usage is:
>
> fiximagedbonds [<mask>]
>
> Using this new command I was able to properly re-image your trajectory
> using the following cpptraj input:
>
> parm 0P.com.wat.leap.prmtop
> trajin 0P.com-sample-frames.nc
> fiximagedbonds
> autoimage
> trajout reimage.nc
>
> Note that I place an 'autoimage' command after 'fiximagedbonds'. This
> is because the way cpptraj fixes the imaged bonds it can lead to
> structures that appear to be outside the box. Once the bonds have been
> fixed 'autoimage' works as intended. Also note that it appears that
> the waters in your system are not imaged by atom. If this is the case
> (i.e. if the water will never have broken bonds) the command can be
> sped up by excluding the waters, e.g.
>
> fiximagedbonds !:WAT
>
> Please let me know if you get a chance to try it and it works (or
> doesn't work). Thanks for the report.
>
> -Dan
>
> PS - GitHub pull request details for those interested here:
> https://github.com/Amber-MD/cpptraj/pull/504
>
>
>
> On Mon, Jun 26, 2017 at 12:06 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> > Thanks for the files, I do see what you mean now. I'm looking into it.
> > I'll get back to you (hopefully) soon.
> >
> > -Dan
> >
> > On Fri, Jun 23, 2017 at 6:55 AM, SHAILESH KUMAR <shaile27_sit.jnu.ac.in>
> wrote:
> >> Thank you Dan!,
> >>
> >> Here I am sharing a tar containing following files:
> >> 0P.com-sample-frames.nc
> >> 0P.com.wat.leap.inpcrd
> >> 0P.com.wat.leap.prmtop
> >> rst2_acemd.inp
> >>
> >> autoimage.cpptraj.in
> >>
> >> Simulation is performed using ACEMD
> >> <http://docs.acellera.com/acemd/usermanual/> simulation package.
> >> Corresponding file used for input is rst2_acemd.inp
> >> wrapping is enabled using
> >> warp all
> >>
> >> It wraps coordinates byatom see here
> >> <http://docs.acellera.com/acemd/usermanual/#apply-
> periodic-boundary-conditions>
> >> .
> >>
> >> Hope it allows to reproduce the problem I am facing.
> >>
> >> https://drive.google.com/file/d/0BxWg4r6noGsRMVpPWjVMazF1RmM/
> view?usp=sharing
> >>
> >> On Thu, Jun 22, 2017 at 9:52 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >>
> >>> Can you describe exactly how the intial 'autoimage' did not work? Your
> >>> best bet for getting help is to provide your exact input and as
> >>> precise a description of the original problem as possible.
> >>>
> >>> -Dan
> >>>
> >>> On Thu, Jun 22, 2017 at 12:47 PM, SHAILESH KUMAR <
> shaile27_sit.jnu.ac.in>
> >>> wrote:
> >>> > I tried autoimage first as it is suggested in manual, but it did not
> >>> > worked. Only after that I tried unwrap & image combination
> >>> >
> >>> > On Jun 22, 2017 5:57 PM, "Daniel Roe" <daniel.r.roe.gmail.com>
> wrote:
> >>> >
> >>> >> What happens if you just 'autoimage' (don't unwrap first)?
> >>> >>
> >>> >> -Dan
> >>> >>
> >>> >> On Thu, Jun 22, 2017 at 9:51 AM, SHAILESH KUMAR <
> shaile27_sit.jnu.ac.in
> >>> >
> >>> >> wrote:
> >>> >> > Dear Fellows,
> >>> >> >
> >>> >> > I have performed a MD simulation with coordinates wrapping
> enabled.
> >>> Now I
> >>> >> > am facing discontinuous trajectory problem. I tried to unwrap
> >>> coordinates
> >>> >> > and reimage but it did not helped. Investigating about the cause
> of
> >>> >> problem
> >>> >> > I found following things.
> >>> >> >
> >>> >> > 1. PBC Box dimensions: {88.588371 75.344688 67.300514 90.000000
> >>> 90.000000
> >>> >> > 90.000000}
> >>> >> > 2. Protein dimension (distance between coordinates of extreme
> points
> >>> in
> >>> >> > protein) as
> >>> >> > {63.625731468200684 49.82566452026367 40.63145446777344}
> >>> >> >
> >>> >> > Unwrapping and Imaging was done as below with cpptraj.
> >>> >> >
> >>> >> > parm com.wat.leap.prmtop
> >>> >> > trajin rst2_out.dcd 1 51000 10
> >>> >> > reference ../../../../02.leap/com/com.wat.leap.inpcrd
> >>> >> > unwrap byres reference !:1-287
> >>> >> > center :123.HE2 mass origin reference
> >>> >> > image origin center familiar com :123.HE2 byres !:1-287
> >>> >> > unwrap byatom reference :1-287
> >>> >> > center :123.HE2 mass origin reference
> >>> >> > image origin center familiar com :123.HE2 byatom :1-287
> >>> >> > trajout com.strip_cr14.nc
> >>> >> > go
> >>> >> >
> >>> >> > Atom :123.HE2 was nearest protein atom to the center of PBC box
> in
> >>> >> initial
> >>> >> > coordinates, hence it was chosen for centering protein to the box.
> >>> >> >
> >>> >> > Now, problem is that molecule has rotated during the simulation
> in the
> >>> >> box
> >>> >> > and hence atoms are crossing two opposite sides of the box at the
> same
> >>> >> > time. So, when it is wrapped these atoms are appearing from
> opposite
> >>> of
> >>> >> > actual side it should be, leading to stretches of structure
> connected
> >>> by
> >>> >> > bonds length of box-dimension.
> >>> >> >
> >>> >> > So, I tried to construct a cubic box of side length 20 with is
> center
> >>> at
> >>> >> > the center of PBC-box.
> >>> >> > as follows.
> >>> >> >
> >>> >> > Let centre of PBC-box has coordinates {cx cy cz}
> >>> >> > then six-set of residues corresponding to residues beyond
> >>> inner-cubic-box
> >>> >> > faces were selected as
> >>> >> >
> >>> >> > set rset1 [atomselect top "protein and x < cx - 10"]
> >>> >> > set rset1 [atomselect top "protein and x > cx + 10"]
> >>> >> > set rset1 [atomselect top "protein and y < cy - 10"]
> >>> >> > set rset1 [atomselect top "protein and y > cy + 10"]
> >>> >> > set rset1 [atomselect top "protein and z < cz - 10"]
> >>> >> > set rset1 [atomselect top "protein and z > cz + 10"]
> >>> >> >
> >>> >> > Now residues in these sets were unwraped
> >>> >> > centering was done with atom closet to the center of corresponding
> >>> face
> >>> >> of
> >>> >> > inner-cubic-box
> >>> >> > and image was done for these set of residues. but it dis not work
> >>> >> >
> >>> >> > Other suggested options were also tried e.g.
> >>> >> >
> >>> >> > unwrap
> >>> >> > autoimage
> >>> >> >
> >>> >> > with bymol, byres and byatom options with solute mask, all system
> >>> mask,
> >>> >> but
> >>> >> > yet to succeed.
> >>> >> >
> >>> >> > Any help and suggestions in regard will be greatly appreciated.
> >>> >> >
> >>> >> > Thank you.
> >>> >> >
> >>> >> > Image of system with/without box waters shown is attached. If
> >>> required, I
> >>> >> > can share, prmtop and dcd files with some frames.
> >>> >> >
> >>> >> > _______________________________________________
> >>> >> > AMBER mailing list
> >>> >> > AMBER.ambermd.org
> >>> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>> >> >
> >>> >>
> >>> >>
> >>> >>
> >>> >> --
> >>> >> -------------------------
> >>> >> Daniel R. Roe
> >>> >> Laboratory of Computational Biology
> >>> >> National Institutes of Health, NHLBI
> >>> >> 5635 Fishers Ln, Rm T900
> >>> >> Rockville MD, 20852
> >>> >> https://www.lobos.nih.gov/lcb
> >>> >>
> >>> >> _______________________________________________
> >>> >> 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
> >>> Laboratory of Computational Biology
> >>> National Institutes of Health, NHLBI
> >>> 5635 Fishers Ln, Rm T900
> >>> Rockville MD, 20852
> >>> https://www.lobos.nih.gov/lcb
> >>>
> >>> _______________________________________________
> >>> 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
> > Laboratory of Computational Biology
> > National Institutes of Health, NHLBI
> > 5635 Fishers Ln, Rm T900
> > Rockville MD, 20852
> > https://www.lobos.nih.gov/lcb
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jun 28 2017 - 11:30:02 PDT
