thanks for the help .. will try<br><br><div class="gmail_quote">On Wed, Jun 15, 2011 at 3:02 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
maria goranovic wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I am using the command:<br>
<br>
trjcat -f *gro -o temp.xtc -cat <br>
to concatenate about 40,000 frames of 14,000 atoms each. The commands works well for 10,000 frames, but crashes for 40,000 frames after reading all the frames. There is sufficient disk space. Is this a bug of some kind? <br>
</blockquote>
<br></div>
Not a bug, but rather clunky code - trjcat consumes a huge amount of memory. If your .gro files are large, then that is the likely limitation. Convert the .gro frames to .xtc with trjconv, then concatenate those instead.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
-- <br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
<br>
</blockquote>
<br></div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<div><div></div><div class="h5"><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen<br>