Hi,
A few things I can think of to try:
1) Important: you must image *before* you rms fit; otherwise your
coordinates are rotated but your unit cell vectors are not. Imaging cannot
be performed after RMS fitting.
2) I'm not sure how you are visualizing the water density, but you may need
to adjust your contour levels.
3) Make sure the grid is large enough to actually capture some water
density.
4) Try using 'autoimage origin' instead of 'center' and 'image'.
Hope this helps,
-Dan
On Tue, Mar 25, 2014 at 12:02 PM, Jio M <jiomm.yahoo.com> wrote:
> Dear Daniel
>
> I am getting trouble with waters.I realised the trajectory should be
> imaged so I added image command (commands shown below). But I dont get any
> waters in spatial distribution but I do get SD for Na and Cl. If I choose
> few frames of trajectory say 10 to 20 then I do get some water molecules.
> Dont know whats happening (though it works fine with only few frames OR
> without using "image origin center familiar")
>
> trajin initial.inpcrd
> principal :1-388 dorotation
> trajout test.aligned.rst7
> run #### STEP1
> clear trajin
> reference test.aligned.rst7
> trajin md.trj
> rms reference mass :1-388
>
> center :1-388 origin
> image origin center familiar
> grid wat_grid.xplor 30 2 30 2 50 2 :WAT.O origin
> grid cl_grid.xplor 30 2 30 2 50 2 :Cl- origin
> grid k_grid.xplor 30 2 30 2 50 2 :Na+ origin
> trajout test_princi_rms.nc nc
>
> run ## STEP 2
>
>
> thanks
> Jiom
>
>
> On Monday, March 24, 2014 9:11 PM, Jio M <jiomm.yahoo.com> wrote:
>
> Dear Daniel
>
> Thanks for replies and help. I extremely apologise as the box looks fine
> and encloses my molecule as expected with the dimensions of my molecule.
> I understood it in wrong way. The nx*dx, ny*dy, nz*dz gives the dimension
> X, Y, Z of box but I was confused and thought that just nx is the X
> dimension and dx should not affect the box size. I should multiply nx with
> dx to get the dimension.
>
> Sorry again and thanks.
>
>
>
> On Monday, March 24, 2014 2:22 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> Hi,
>
> On Sat, Mar 22, 2014 at 8:35 PM, Jio M <jiomm.yahoo.com> wrote:
>
> > Thanks its working fine now, but the only thing is polymer Z dimension is
> > around 100 Angs and if I use:
> > grid wat_grid.xplor 30 2 30 2 100 2
> >
> > then the xplor box Z dimension is 20 to 30 Angs longer than Z dimension
> of
> > my polymer. So I have to reduce it like this to fit in xplor box:
> >
> > grid wat_grid.xplor 30 2 30 2 80 2
> >
>
> FYI the upcoming version of cpptraj will have an additional option to
> center the grid at a specific location (offset from the origin), which I
> think will help in this situation.
>
>
> > Also one more thing earlier version of 'grid' was not programmed to
> > average over same atom. e.g. for spatial distribution of Cl- ions around
> > Na+, one needs to calculate on single Na+ ion by centring it then
> averaging
> > for all by own script (as suggested by archive mails). Is it possible now
> > just by giving wild mask? thats is
> > center :Na+ origin ## expected to average ??
> >
>
> No, grid does not currently have an option to do this. However, the
> upcoming version of cpptraj will allow you to append to a previously
> defined grid data set, so you should eventually be able to do this.
>
> -Dan
>
>
> >
> > OR
> >
> > center :389 origin ## just for one ion (where 389 is Na+ number)
> >
> >
> > Thanks a lot
> > Jiom
> >
> >
> > On Saturday, March 22, 2014 10:01 PM, Daniel Roe <daniel.r.roe.gmail.com
> >
> > wrote:
> >
> > Hi,
> >
> > Without knowing exactly what your trajectory looks like it's tough to
> make
> > an exact diagnosis, but I suspect there may be an issue as to where the
> > grid is centered. In your second step try centering your solute at the
> > origin after the origin command, then try to create the grid (no need
> for a
> > step 3) placing the center of your grid at the origin as well, e.g.:
> >
> > ...
> > rms reference mass :1-388
> > center :1-388 origin
> > grid wat_grid.xplor 60 2 60 2 100 2 :WAT.O origin
> > trajout test_princi_rms.nc nc
> > run ### STEP2
> >
> > Hope this helps,
> >
> > -Dan
> >
> >
> >
> >
> > On Sat, Mar 22, 2014 at 12:43 PM, Jio M <jiomm.yahoo.com> wrote:
> >
> > > Dear All
> > >
> > > I have a long polymer around 100 Angs length and 60 Angs diameter with
> > 388
> > > resdiues and in octahedron water/ions box. I want to calculate spatial
> > > distribution of water along the length using grid option (following
> some
> > > archive mail: http://archive.ambermd.org/201109/0613.html)
> > >
> > > So I have run following cpptraj commands for just 10 frames for test:
> > > (first two runs are for aligning along Z which works fine and was
> kindly
> > > suggested by Daniel few weeks before; final third run is for grids):
> > >
> > >
> > > trajin initial.inpcrd
> > > principal :1-388 dorotation
> > > trajout test.aligned.rst7
> > > run #### STEP1
> > > clear trajin
> > > reference test.aligned.rst7
> > > trajin md.trj 1 10
> > > rms reference mass :1-388
> > > trajout test_princi_rms.nc nc
> > > run ### STEP2
> > > clear trajin
> > > trajin test_princi_rms.nc
> > > rms reference mass :1-388 #### I have tried with and without this rms
> > > option; which is rather a repeat
> > > grid wat_grid.xplor 60 2 60 2 100 2 :WAT.O box ### Note different Z
> > > dimension
> > > run ### STEP3
> > >
> > > I am getting following problem:
> > >
> > > Using netcdf trajcteory I have checked that I get good Z-aligned
> > structure
> > > (visually seen STEP2 traj file: test_princi_rms.nc) and I expect water
> > to
> > > be aligned along Z axis too and make an outline shape corresponding to
> > the
> > > length of polymer. Xplor file in VMD shows the water distribution gets
> > the
> > > outline shape of polymer but not aligned along the Z axis and also I
> see
> > > clump of points at the corner of box (something observed when long
> > molecule
> > > is not imaged properly and looks broken in parts).
> > >
> > > thanks a lot
> > > Jiom
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 201
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> > _______________________________________________
> > 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, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
> _______________________________________________
> 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
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Mar 25 2014 - 12:30:03 PDT
