Nilesh Dhumal wrote:
Hey Justin,
I have a small query. I have total 128 pairs of ionic liquids. THats why
most of the group have more that 3 elements. Now If I manually make the
groups with 2 or 3 elements (which is really hard and no. groups will be
more than 1000)then How can I take the average.
Have a look at g_sorient, as well; it may serve you better.
-Justin
Nilesh
On Fri, December 11, 2009 9:22 pm, Justin A. Lemkul wrote:
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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Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]. Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
--
========================================
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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