How big is your file? Technically you might not be able to load the file if it is larger than you machine's memory.
One way to deal with this is converting the file (xtc or trr) not to include solvent. If that is indeed the case, I suggest you create a group that contains everything you have in the simulation except for the solvent and then run: trjconv -f file.xtc -o file_without_water.xtc -n index.ndx You will be asked to choose a group - choose the group you created without the water. Now do the same to your .gro file (so there would be the same number of atoms in gro and in the xtc), and you should be able to load the entire "no-water" xtc without problems. -Shay _____ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of minnale Sent: Sunday, August 17, 2008 08:30 AM To: gmx-users1 Subject: Re: Re: [gmx-users] problem with protein secondary structure analysis 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/signatur e-default.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3&OAS_QUE RY=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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