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<BR>
Thanks to Justin for his prompt reply<BR>
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.<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 and performed these steps.<BR>
>>1. First loaded min.gro file and corresponding min.xtc then all 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 subtrajectories with 1ns interval by using *trjconv command and issued like 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 (2725)<BR>
><BR>
>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.<BR>
><BR>
>-Justin<BR>
><BR>
>><BR>
>>Could you please give me suggestion if any one have experienced this type of problem<BR>
>>Thanks in advance.<BR>
>><BR>
>><BR>
>><BR>
>>Rediff Shopping <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/1050715198@Middle5/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null><BR>
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>-- ========================================<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>
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