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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Received on Sat Mar 22 2014 - 12:00:02 PDT
