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. 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 >>>>> >>>>> >>>>> >>>>> >>>>> ======================================== >>>>> -- >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>> 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-requ...@gromacs.org. >>>>> 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 >>> >>> >>> >>> ======================================== >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> 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-requ...@gromacs.org. 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 > > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > 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-requ...@gromacs.org. Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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-requ...@gromacs.org. Can't post? 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