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Hi Dallas,<br>
<br>
Thank for the replay. I think that I found what was "wronge". I have
created the tpr files using GROMACS 3.3.3 but used gmxdump (-sys) from
the GROMACS 4.0.5 package, not a very smart thing to do, ha? I guess
this was the source of my error.<br>
<br>
<br>
Thanks,<br>
Itamar<br>
<br>
<br>
On 21/01/10 1:36 PM, Dallas B. Warren wrote:
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<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Might
be a good idea to provide the input and output that
generated the error.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Catch
ya,<br>
<br>
Dr. Dallas Warren<br>
</span><span
style="font-size: 10pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Drug
Delivery, Disposition and Dynamics</span><span
style="font-size: 10pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><br>
</span><span
style="font-size: 10pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Monash
Institute of Pharmaceutical Sciences</span><span
style="font-size: 10pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">,
Monash
University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a class="moz-txt-link-abbreviated" href="mailto:dallas.warren@pharm.monash.edu.au">dallas.warren@pharm.monash.edu.au</a><br>
+61 3 9903 9167<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to
resemble a
nail.</span><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";">
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>
[<a class="moz-txt-link-freetext" href="mailto:gmx-users-bounces@gromacs.org">mailto:gmx-users-bounces@gromacs.org</a>] <b>On Behalf Of </b>Itamar Kass<br>
<b>Sent:</b> Thursday, 21 January 2010 11:13 AM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> [gmx-users] atomnumber=-12345<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi,<br>
<br>
After one of my simulation had crashed, I had used gmxdump to look into
it. What stoke me was the all atoms have the same atomnumer:<br>
atom[ 0]={type= 0, typeB= 0,
ptype= Atom, m= 1.40067e+01, q= 1.29000e-01, mB= 1.40067e+01,
qB= 1.29000e-01, resnr= 0, atomnumber=-12345}<br>
atom[
1]={type= 1, typeB= 1, ptype= Atom, m=
1.00800e+00, q= 2.48000e-01, mB= 1.00800e+00, qB= 2.48000e-01,
resnr= 0, atomnumber=-12345}<br>
atom[
2]={type= 1, typeB= 1, ptype= Atom, m=
1.00800e+00, q= 2.48000e-01, mB= 1.00800e+00, qB= 2.48000e-01,
resnr= 0, atomnumber=-12345}<br>
atom[
3]={type= 1, typeB= 1, ptype= Atom, m=
1.00800e+00, q= 2.48000e-01, mB= 1.00800e+00, qB= 2.48000e-01,
resnr= 0, atomnumber=-12345}<br>
atom[
4]={type= 2, typeB= 2, ptype= Atom, m=
1.30190e+01, q= 1.27000e-01, mB= 1.30190e+01, qB= 1.27000e-01,
resnr= 0, atomnumber=-12345}<br>
<br>
<br>
and so on...<br>
<br>
I wonder if someone knows what the origin of this error and how to over
come
it?<br>
<br>
In addition, it is vary strange that the simulation run for 100ps
before it
crashed. <br>
<br>
All the best,<br>
Itamar.<br>
<br>
<br>
<span class="moz-txt-tag">-- </span><br>
<br>
<br>
"In theory, there is no difference between theory and practice. But, in
practice, there is." - Jan L.A. van de Snepscheut <br>
<br>
=========================================== <br>
| Itamar Kass, Ph.D. <br>
| Postdoctoral Research Fellow <br>
| <br>
| Department of Biochemistry and Molecular Biology <br>
| Building 77 Clayton Campus <br>
| Wellington Road <br>
| Monash University, <br>
| Victoria 3800 <br>
| Australia <br>
| <br>
| Tel: +61 3 9902 9376 <br>
| Fax: +61 3 9902 9500 <br>
| E-mail: <a moz-do-not-send="true"
href="mailto:Itamar.Kass@med.monash.edu.au">Itamar.Kass@med.monash.edu.au</a>
<br>
============================================ <o:p></o:p></p>
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