Nilesh Dhumal wrote:
Hello,
I have a system with glucose + ionic liquids (cation + anion).
I am trying calculate distribution of cation and anion around glucose
molecule using g_sdf. I want to plot distribution of cation and anion is
same figure. I run the following command
g_sdf -f 3.trr -s 3.tpr -n glu-emi-dmp-128-no.ndx -mode 2 -o -r
I selected two atoms from glucose and 3rd and 4th groups are cation and
anion respectively.
All the coordinates in refmol.gro are zero.
I am using gromacs version 4.0.7.
Why all the coordinates in refmol.gro are zero.
g_sdf is relatively inflexible; it was designed (it appears) around calculations
involving water. g_spatial is much more flexible, and I believe it was for this
reason that g_sdf has been removed from newer Gromacs versions. Try g_spatial
instead.
-Justin
--
========================================
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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