[gmx-users] Regarding calculation of Spatial Distribution Function

[Dilip H N]

Hello,
I want to do the Spatial Distribution Function,
I tried to follow the manual gmx spatial.....
I am following the five-step protocol which is given in gmx spatial manual..
1) I have an index file ndx_CaOw.ndx (which contains the C-alpha and all
the Ow's of water molecules, Is this index good or should i have all the
molecules..??)
2) in the second step-  "gmx trjconv -s a.tpr
<http://manual.gromacs.org/online/tpr.html> -f a.tng
<http://manual.gromacs.org/online/tng.html> -o b.tng
<http://manual.gromacs.org/online/tng.html> -boxcenter tric -ur compact
-pbc none" here we need to give the input file ie., -f a.tng from where
does this .tng file i need to give the input..?? How do i create a .tng
file.. what information does this tng file contain...??

Any suggestions...

Thank you.
-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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