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
>>
> _______________________________________________
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> 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
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Received on Mon Jun 26 2017 - 09:30:02 PDT
