[gmx-users] g_sdf

[Justin A. Lemkul]

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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