Hi Shay and Justin Thanks for your clear suggestion your suggested way is working fine. Thanks alot once again.
On Sun, 17 Aug 2008 Shay Amram wrote : >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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