Nilesh Dhumal wrote:
Hello,
I am trying to calculate g_sdf for my system (ionic liquids + water).
I interested in distribution of anions and waters around cations.
I used following command
g_sdf -f 3.trr -n emi-etso4-64-no.ndx -s 3.tpr -o -r -mode 2
I found all the corrdinates in refmol.gro are zero.
I calculated distribution of anions around cations
g_sdf -f 3.trr -n emi-etso4-64-no.ndx -s 3.tpr -o -r
I got proper corrdinates in refmol.gro.
Why I am getting corrdinates zero for mode 2.
You're not using the command properly. Read g_sdf -h.
You may find g_spatial more useful; in fact, g_sdf has been removed from version
4.5 while g_spatial was maintained. g_sdf is better suited for water and not
much else.
-Justin
Nilesh
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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