Nilesh Dhumal wrote:
hey Justin,
I tried to plot between the groups are planar. But still its giving me
same error
mk_angndx -s 3.tpr -n angle.ndx -type angle (COmmand used for angle.ndx
file)
g_sgangle -f 3.xtc -n angle.ndx -s 3.tpr -oa test.xvg
Fatal error: Something wrong with contents of index file.
My previous reply is still applicable. To do the analysis you want, you may
have to (by hand) define custom index groups (see the points I raised below).
The requirements for proper index file content are spelled out in the g_sgangle
help information and the manual.
-Justin
Nilesh
On Fri, December 11, 2009 3:03 pm, Justin A. Lemkul wrote:
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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--
========================================
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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