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<p class=MsoNormal dir=LTR><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>How big is your file? <o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>Technically you might not be able to load the file if it is
larger than you machine's memory.<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>One way to deal with this is converting the file (xtc or
trr) not to include solvent. <o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>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:<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-indent:.5in'><b><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial;font-weight:bold'>trjconv –f file.xtc
–o file_without_water.xtc –n index.ndx</span></font></b><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>You will be asked to choose a group – choose the group
you created without the water.<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>-Shay<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
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<p class=MsoNormal dir=LTR><b><font size=2 face=Tahoma><span style='font-size:
10.0pt;font-family:Tahoma;font-weight:bold'>From:</span></font></b><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b><span
style='font-weight:bold'>On Behalf Of </span></b>minnale <br>
<b><span style='font-weight:bold'>Sent:</span></b> Sunday, August 17, 2008
08:30 AM<br>
<b><span style='font-weight:bold'>To:</span></b> gmx-users1<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: Re: [gmx-users]
problem with protein secondary structure analysis</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p dir=LTR><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>
<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
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>><br>
>><br>
>>------------------------------------------------------------------------<br>
>><br>
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><br>
>-- ========================================<br>
><br>
>Justin A. Lemkul<br>
>Graduate Research Assistant<br>
>Department of Biochemistry<br>
>Virginia Tech<br>
><st1:place w:st="on"><st1:City w:st="on">Blacksburg</st1:City>, <st1:State
w:st="on">VA</st1:State></st1:place><br>
>jalemkul[at]vt.edu | (540) 231-9080<br>
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>
><br>
>========================================<o:p></o:p></span></font></p>
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