Hi,
I'm trying to check the ion occupancy of the md trajectory file, but all I
got was zero density at every point.
My ptraj file is below
=========================
trajin ZNA_WAT.mdcrd
center :1 origin
image origin center familiar
rms first out ':1-12 & !.H='
grid Z_ion.xplor 200 0.5 200 0.5 200 0.5 ':Na+'
=========================
I could not understand the "200 0.5 200 0.5 200 0.5" part on the last line.
When I assign 'nx', why do I need 'x_spacing', or when I assign spacing, why
do I need to assign nx?
I guess I misunderstood something on this.
Then, how could I assign this grid point appropriately?
I do not know if this Is the reason that I got wrong result for the ion
occupancy.
I also attach the ptraj file for extracting pdb file which does not contain
the ions.
=========================
trajin ZNA_WAT.mdcrd 1 1 1
trajout ZNA_avr.pdb pdb
center :1 origin
image origin center familiar
strip :13-99999999
translate x 0.25 y 0.25 z 0.25
=========================
Thank you
Sincerely, YounKyoung.Seoul National University
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Received on Tue Jul 21 2009 - 01:09:34 PDT
