<br clear="all"><br>--<br>Chandan kumar Choudhury<br>NCL, Pune<br>INDIA<br>
<br><br><div class="gmail_quote">On Fri, Dec 24, 2010 at 3:13 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div text="#000000" bgcolor="#ffffff"><div class="im">
On 24/12/2010 4:58 AM, Chandan Choudhury wrote:
<blockquote type="cite">Hello all !!
<div><br>
</div>
<div>I have a 30 ns trajectory in two parts (0-20 & 20-30). I
am using Gromacs 4.0.7. I concatenated using trjcat (<b>echo 2 |
trjconv -s md10-30.tpr -f 0-30.trr -o pbc_whole.trr -n
index_grdf.ndx -nice 0</b>). <br>
</div>
</blockquote>
<br></div>
That looks like subset creation, not concatenation. Perhaps you
should clarify what you think should be in all these files, and
confirm with gmxcheck.</div></blockquote><div><br></div><div>Sorry. I wrongly copied the commands. The correct command was <b>trjcat -f 0-20.trr 20-30/20-30.trr -o analysis/0-30/0-30.trr -nice 0</b></div><div><b>gmxcheck -f pbc_whole.trr </b>outputs</div>
<div><br></div><div>Checking file pbc_whole.trr</div><div>trn version: GMX_trn_file (single precision)</div><div>Reading frame 0 time 0.000 </div><div># Atoms 162</div><div>Last frame 300000 time 30000.002 </div>
<div> </div><div>Item #frames Timestep (ps)</div><div>Step 300001 0.1</div><div>Time 300001 0.1<br>Lambda 300001 0.1</div><div>Coords 300001 0.1</div><div>Velocities 300001 0.1</div>
<div>Forces 0</div><div>Box 300001 0.1</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div text="#000000" bgcolor="#ffffff"><div class="im">
<blockquote type="cite"><div>Then I converted the concatenated trajectory into pbc
trajectory using trjconv (<b>echo 2 | trjconv -f 0-30.trr -s
md10-30.tpr -o pbc_whole.trr -n index_grdf.ndx -pbc whole</b>).
The problem comes when I try to use the g_polystat utility (<b>echo
2 |</b> <b>g_polystat -s md10-30.tpr -f pbc_whole.trr -n
index_grdf.ndx -o polystat_pbc.dat -xvgr</b>). The error
message it produces is :</div>
<div><i>trn version: GMX_trn_file (single precision)</i></div>
<div><i>Reading frame 0 time 0.000 </i></div>
<div><i>-------------------------------------------------------</i></div>
<div><i>Program g_dist, VERSION 4.0.7</i></div>
<div><i>Source code file: mshift.c, line: 103</i></div>
<div><i><br>
</i></div>
<div><i>Fatal error:</i></div>
<div><i>Molecule in topology has atom numbers below and above
natoms (162).</i></div>
<div><i>You are probably trying to use a trajectory which does not
match the first 162 atoms of the run input file.</i></div>
<div><i>You can make a matching run input file with tpbconv.</i></div>
<div>-------------------------------------------------------</div>
</blockquote>
<br></div>
This means the contents of at least two of the .trr, .tpr and .ndx
aren't describing the same thing.<br><font color="#888888">
<br>
Mark</font><div class="im"><br>
<br>
<blockquote type="cite">
<div>The same error message erupts when I try to use g_dist. (echo
"5 24" | g_dist -f pbc_whole.trr -s md10-30.tpr -n
index_grdf.ndx -o dist_N-N.xvg).</div>
<div><br>
</div>
<div><br>
</div>
<div>But when I execute g_mindist (echo "5 24" | g_mindist -f
pbc_whole.trr -s md10-30.tpr -n index_grdf.ndx -o
mindist_N-N.xvg). I works w/o any error message.</div>
<div><br>
</div>
<div>Can figure out the probable cause. Please help.</div>
<div><br>
--<br>
Chandan kumar Choudhury<br>
NCL, Pune<br>
INDIA<br>
</div>
</blockquote>
<br>
</div></div>
<br>--<br>
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