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
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> 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)
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Received on Tue Mar 25 2014 - 12:30:02 PDT
