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. 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 [email protected] >>> 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 [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 > > > ======================================== > -- > gmx-users mailing list [email protected] > 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 [email protected]. Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
