Dear Daniel
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
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 ??
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
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>
--
-------------------------
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 Sat Mar 22 2014 - 20:00:02 PDT
