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<BR>
Hi Shay and Justin Thanks for your clear suggestion <BR>
your suggested way is working fine.<BR>
Thanks alot once again. <BR>
<BR>
<BR>
<BR>
On Sun, 17 Aug 2008 Shay Amram wrote :<BR>
>How big is your file?<BR>
><BR>
>Technically you might not be able to load the file if it is larger than you<BR>
>machine's memory.<BR>
><BR>
>One way to deal with this is converting the file (xtc or trr) not to include<BR>
>solvent.<BR>
><BR>
>If that is indeed the case, I suggest you create a group that contains<BR>
>everything you have in the simulation except for the solvent and then run:<BR>
><BR>
>trjconv -f file.xtc -o file_without_water.xtc -n index.ndx<BR>
><BR>
><BR>
><BR>
>You will be asked to choose a group - choose the group you created without<BR>
>the water.<BR>
><BR>
>Now do the same to your .gro file (so there would be the same number of<BR>
>atoms in gro and in the xtc), and you should be able to load the entire<BR>
>"no-water" xtc without problems.<BR>
><BR>
><BR>
><BR>
>-Shay<BR>
><BR>
><BR>
><BR>
> _____<BR>
><BR>
> From: gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]<BR>
>On Behalf Of minnale<BR>
>Sent: Sunday, August 17, 2008 08:30 AM<BR>
>To: gmx-users1<BR>
>Subject: Re: Re: [gmx-users] problem with protein secondary structure<BR>
>analysis<BR>
><BR>
><BR>
><BR>
><BR>
>Thanks to Justin for his prompt reply<BR>
>in .mdp file mentioned energy groups and tc-grps are protein and sol_cl . I<BR>
>am in doubt that first 250ps of md run it in npt condition later nvt till<BR>
>7ns finally made into long .xtc file.<BR>
>I tried your suggested way in earlier post but I didnt get it.<BR>
><BR>
>one more doubt I am having is<BR>
>If I load entire .xtc file which contain 7ns trajectory it didnt load<BR>
>Could please tell me why its not loading<BR>
>Thanks in advance.<BR>
><BR>
><BR>
>On Sat, 16 Aug 2008 Justin A.Lemkul wrote :<BR>
> ><BR>
> ><BR>
> >minnale wrote:<BR>
> >> Hi all,<BR>
> >> I intersted in analysing secondary structure of protein by using VMD<BR>
>and performed these steps.<BR>
> >>1. First loaded min.gro file and corresponding min.xtc then all<BR>
>equalibration .xtc files till here MD movie has run fine.<BR>
> >>2. I had long trajectory in a single file, so cut it down into<BR>
>subtrajectories with 1ns interval by using *trjconv command and issued like<BR>
>this<BR>
> >> trjconv -f .xtc -o 1ns.xtc -s .tpr -b 0 -e 1000<BR>
> >> selected system, it showed<BR>
> >><BR>
> >>Fatal error:<BR>
> >>Index[2725] 2726 is larger than the number of atoms in the trajectory file<BR>
>(2725)<BR>
> ><BR>
> >You've only saved a subset of your trajectory. Check the xtc-grps in your<BR>
>.mdp file. You can use trjconv if you have a reference structure that<BR>
>matches the contents of your trajectory.<BR>
> ><BR>
> >-Justin<BR>
> ><BR>
> >><BR>
> >>Could you please give me suggestion if any one have experienced this type<BR>
>of problem<BR>
> >>Thanks in advance.<BR>
> >><BR>
> >><BR>
> >><BR>
> >>Rediff Shopping<BR>
><http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signatur<BR>
>e-default.htm/1050715198@Middle5/2206641_2199021/2201651/1?PARTNER=3&OAS_QUE<BR>
>RY=null><BR>
> >><BR>
> >><BR>
> >>------------------------------------------------------------------------<BR>
> >><BR>
> >>_______________________________________________<BR>
> >>gmx-users mailing list gmx-users@gromacs.org<BR>
> >>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>
> >>Please search the archive at http://www.gromacs.org/search before posting!<BR>
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> >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>
> ><BR>
> >-- ========================================<BR>
> ><BR>
> >Justin A. Lemkul<BR>
> >Graduate Research Assistant<BR>
> >Department of Biochemistry<BR>
> >Virginia Tech<BR>
> >Blacksburg, VA<BR>
> >jalemkul[at]vt.edu | (540) 231-9080<BR>
> >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>
> ><BR>
> >========================================<BR>
><BR>
><BR>
><BR>
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