Hi Dan,
Sorry for delayed response.
I was out of town and did not had access to trajectories to test the
implemented command fiximagedbonds.
After returning, I tested command fiximagedbonds on my trajectoryes, and it
is working fine.
Thank you again for implementing this command. It is a great help.
On Wed, Jun 28, 2017 at 8:02 PM, SHAILESH KUMAR <shaile27_sit.jnu.ac.in>
wrote:
> 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
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Thu Jul 13 2017 - 14:30:03 PDT
