<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#ffffff">
On 24/12/2010 4:58 AM, Chandan Choudhury wrote:
<blockquote
cite="mid:AANLkTi=Q1-artoVZPH1j3Czji=AQvr8VwG6JpbqXUb0V@mail.gmail.com"
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>
That looks like subset creation, not concatenation. Perhaps you
should clarify what you think should be in all these files, and
confirm with gmxcheck.<br>
<br>
<blockquote
cite="mid:AANLkTi=Q1-artoVZPH1j3Czji=AQvr8VwG6JpbqXUb0V@mail.gmail.com"
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>
This means the contents of at least two of the .trr, .tpr and .ndx
aren't describing the same thing.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTi=Q1-artoVZPH1j3Czji=AQvr8VwG6JpbqXUb0V@mail.gmail.com"
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>
</body>
</html>