[gmx-users] plot of mutual orienatation
Justin A. Lemkul
jalemkul at vt.edu
Fri Dec 11 21:03:30 CET 2009
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.
> 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
>> Try g_sgangle.
>> 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
>> gmx-users mailing list gmx-users at gromacs.org
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org. Can't post? Read
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users