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
>
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Received on Fri Jun 23 2017 - 04:00:02 PDT
