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On 8/12/2011 5:04 PM, Chandan Choudhury wrote:
<blockquote
cite="mid:CAHESojxF2sK4c3yWzSfz_u=mAzq3mOdZGBGDMkHyVH-W0sg4yg@mail.gmail.com"
type="cite">For any text file, use your favorite editor to delete
all your water molecules. It will load very fast. For the xtc/trr
files, use trjconv with an index file to write a new xtc/trr file
without water molecules. Index file should contain the atom nos.
of the molecules you want.
<div>
<br>
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<div>trjconv -s a.tpr -f a.xtc/trr -n a.ndx -o b.xtc/trr</div>
</blockquote>
<br>
Indeed, and the OP may wish to consider the advice here <a
href="http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume">http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume</a><br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAHESojxF2sK4c3yWzSfz_u=mAzq3mOdZGBGDMkHyVH-W0sg4yg@mail.gmail.com"
type="cite">
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<div>chandan<br clear="all">
<br>
--<br>
Chandan kumar Choudhury<br>
NCL, Pune<br>
INDIA<br>
<br>
<br>
<div class="gmail_quote">On Thu, Dec 8, 2011 at 10:56 AM, Saba
Ferdous <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:saba.bsbi154@iiu.edu.pk">saba.bsbi154@iiu.edu.pk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex;">
Dear Sir,<br>
I need to ask you that if I want only pdb coordinates in the
resultant md-noPBC.xtc/md-noPBC.pdb file rather than the
solvant atoms and coordinates then what should I do. because
the water box causes very delay in loading of frames and its
difficult to viualize the trajectory. kindly help me to get
out of the broblem. I only want that my protein get display
in vmd rather than the water box.<br>
the size of md-noPBC.xtc is 612 Mb<br>
md-noPBC.pdb is 13.2 GB<br>
<br>
analysis is getting very slow and system is hanging. kindly
help me out to fix this problem.<br>
<br>
Regards <br>
Thanks<span class="HOEnZb"><font color="#888888"><br>
<br clear="all">
<br>
-- <br>
Saba Ferdous
<div>
Research Scholar (M. Phil)</div>
<div>National Center for Bioinformatics</div>
<div>Quaid-e-Azam University, Islamabad</div>
<div>Pakistan</div>
<br>
</font></span><br>
--<br>
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