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1) trjconv with the "-pbc nojump" option does not help - it removes
most of the jumps but one big remains- the rmsd for the trajectory is<br>
<a class="moz-txt-link-freetext" href="http://www.meduniwien.ac.at/msi/biosim/bk/4.jpg">http://www.meduniwien.ac.at/msi/biosim/bk/4.jpg</a><br>
before the converting with -pbc and<br>
<a class="moz-txt-link-freetext" href="http://www.meduniwien.ac.at/msi/biosim/bk/4noJump.jpg">http://www.meduniwien.ac.at/msi/biosim/bk/4noJump.jpg</a><br>
after conversion.<br>
<br>
interestingly under linux vmd could load the trajectories which look
like that:<br>
<a class="moz-txt-link-freetext"
href="http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1767.jpg">http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1767.jpg</a><br>
and<br>
<a class="moz-txt-link-freetext"
href="http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1768.jpg">http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1768.jpg</a><br>
<br>
2) Here an illustration for other trajectories with the same problem:<br>
<a class="moz-txt-link-freetext" href="http://www.meduniwien.ac.at/msi/biosim/bk/1.jpg">http://www.meduniwien.ac.at/msi/biosim/bk/1.jpg</a><br>
<a class="moz-txt-link-freetext" href="http://www.meduniwien.ac.at/msi/biosim/bk/2.jpg">http://www.meduniwien.ac.at/msi/biosim/bk/2.jpg</a><br>
<a class="moz-txt-link-freetext"
href="http://www.meduniwien.ac.at/msi/biosim/bk/jumppoint.jpg">http://www.meduniwien.ac.at/msi/biosim/bk/jumppoint.jpg</a><br>
<br>
<br>
3) gmxcheck returns no error, just this:<br>
<br>
trn version: GMX_trn_file (single precision)<br>
Reading frame 0 time 0.000 <br>
# Atoms 167731<br>
Reading frame 20000 time 60000.000 <br>
<br>
Item #frames Timestep (ps)<br>
Step 20261 3<br>
Time 20261 3<br>
Lambda 20261 3<br>
Coords 20261 3<br>
Velocities 2027 30<br>
Forces 2027 30<br>
Box 20261 3<br>
<br>
<br>
<a class="moz-txt-link-freetext"
href="http://www.meduniwien.ac.at/msi/biosim/bk/jumppoint.jpg"></a>any
further ideas what I could do with those trajectories or what I shall
do to avoid such problems in future (integration step, water shell
size, ... ?)<br>
<br>
cheers<br>
Bernhard<br>
<br>
<br>
<br>
<pre class="moz-signature" cols="72">
</pre>
<br>
<br>
<br>
<pre wrap="">------------------------------
Message: 4
Date: Mon, 22 Jun 2009 16:37:44 +0200
From: Erik Marklund <a class="moz-txt-link-rfc2396E"
href="mailto:erikm@xray.bmc.uu.se"><erikm@xray.bmc.uu.se></a>
Subject: Re: [gmx-users] problems with some calculated trajectories
To: Discussion list for GROMACS users <a class="moz-txt-link-rfc2396E"
href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
Message-ID: <a class="moz-txt-link-rfc2396E"
href="mailto:4A3F9738.7070103@xray.bmc.uu.se"><4A3F9738.7070103@xray.bmc.uu.se></a>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi,
Could it be a periodicity issue? Have you tried using trjconv -pbc nojump ?
/Erik</pre>
<br>
<br>
<blockquote cite="mid20090623051143.7C83A24833@struktbio205.bmc.uu.se"
type="cite">
<pre wrap="">------------------------------
Message: 2
Date: Mon, 22 Jun 2009 17:19:43 +0200
From: Martin H?fling <a class="moz-txt-link-rfc2396E" href="mailto:martin.hoefling@lmu.de"><martin.hoefling@lmu.de></a>
Subject: Re: [gmx-users] problems with some calculated trajectories
To: Discussion list for GROMACS users <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:806BD6CF-4903-465F-A2B6-8D0FFA98451D@lmu.de"><806BD6CF-4903-465F-A2B6-8D0FFA98451D@lmu.de></a>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Hey Bernhard, here some thoughts of mine:
In principle, vmd should be able to read the trajectories if pdb2gmx
tells you that the trajectory is ok. If this is not the case, you can
use gmx_rescue64 to extract the undamaged parts.
Reasons for damaged trajectories, even when gromacs runs through fine...
... for me - filesystem issues were causing this. In particular this
happened for me with NFS shares and on Lustre filesystems. My NFS
problems got solved with an upgrade of the NFS packages on our
machines (at least 1 1/2 yrs ago).
Best
Martin
------------------------------
Message: 3
Date: Mon, 22 Jun 2009 18:06:13 +0200
From: Martin H?fling <a class="moz-txt-link-rfc2396E" href="mailto:martin.hoefling@gmx.de"><martin.hoefling@gmx.de></a>
Subject: Re: [gmx-users] problems with some calculated trajectories
To: Discussion list for GROMACS users <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:D1212DF6-6341-45D3-8EF6-F975B68CE374@gmx.de"><D1212DF6-6341-45D3-8EF6-F975B68CE374@gmx.de></a>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes
Am 22.06.2009 um 17:19 schrieb Martin Höfling:
</pre>
<blockquote type="cite">
<pre wrap="">Hey Bernhard, here some thoughts of mine:
In principle, vmd should be able to read the trajectories if pdb2gmx
tells you that the trajectory is ok. If this is not the case, you
can use gmx_rescue64 to extract the undamaged parts.
</pre>
</blockquote>
<pre wrap=""><!----> ^
^^^^^^^^^^
= gmxcheck :-)
Best
Martin
------------------------------
Message: 4
Date: Mon, 22 Jun 2009 13:29:10 -0400
From: "Justin A. Lemkul" <a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a>
Subject: Re: [gmx-users] -bash:
/home_soft/soft_chem/soft_install/gromac/bin/GMXRC.bash: No such file
or directory
To: Discussion list for GROMACS users <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:4A3FBF66.4010602@vt.edu"><4A3FBF66.4010602@vt.edu></a>
Content-Type: text/plain; charset=GB2312
</pre>
<br>
</blockquote>
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