Nilesh Dhumal wrote:
I tried to to run g_sgangle.
g_sgangle -f 3.xtc -n ac128-no.ndx -s 3.tpr -od test.xvg
But its giving me following error
Fatal error: Something wrong with contents of index file.
I have ploted the rdf with same index file.
Can you tell me where is the problem
The help information printed by g_sgangle describes the exact requirements. You
may or may not be able to get what you want. Is the angle between the glucose
ring and your 5-membered ring something that is easily described? Glucose is
not planar, so unless you get somewhat creative with the atoms used to describe
its ring system, it may not be possible to calculate such an angle.
-Justin
Nilesh
On Fri, December 11, 2009 2:03 pm, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
Hey All,
I am trying to analyze the results of my simulation. I have used the
ionic liquid as a solvent which have five member ring. I have a glucose
molecule surrounded by ionic liquids. I want to see to plot a angle
between the center of mass of glucose and center of five member ring.
How can I plot
the angle between the center of mass of five member sing sothat I can
study of orientation of ionic liquids in presence and absence of
glucose. I have run the simulation only of ionic liquids. I tried with
g_angle.
Try g_sgangle.
-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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========================================
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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