Thanks to Justin for his prompt reply in .mdp file mentioned energy groups and tc-grps are protein and sol_cl . I am in doubt that first 250ps of md run it in npt condition later nvt till 7ns finally made into long .xtc file. I tried your suggested way in earlier post but I didnt get it.
one more doubt I am having is If I load entire .xtc file which contain 7ns trajectory it didnt load Could please tell me why its not loading Thanks in advance. On Sat, 16 Aug 2008 Justin A.Lemkul wrote : > > >minnale wrote: >> Hi all, >> I intersted in analysing secondary structure of protein by using VMD and >> performed these steps. >>1. First loaded min.gro file and corresponding min.xtc then all >>equalibration .xtc files till here MD movie has run fine. >>2. I had long trajectory in a single file, so cut it down into >>subtrajectories with 1ns interval by using *trjconv command and issued like >>this >> trjconv -f .xtc -o 1ns.xtc -s .tpr -b 0 -e 1000 >> selected system, it showed >> >>Fatal error: >>Index[2725] 2726 is larger than the number of atoms in the trajectory file >>(2725) > >You've only saved a subset of your trajectory. Check the xtc-grps in your >.mdp file. You can use trjconv if you have a reference structure that matches >the contents of your trajectory. > >-Justin > >> >>Could you please give me suggestion if any one have experienced this type of >>problem >>Thanks in advance. >> >> >> >>Rediff Shopping >><http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL >> PROTECTED]/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null> >> >> >>------------------------------------------------------------------------ >> >>_______________________________________________ >>gmx-users mailing list [email protected] >>http://www.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 >Graduate Research Assistant >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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