I didn't un out of disk space but the size of my concatenated .xtc file is 4 GB.<br>Why? the size of my file affects trjconv?<br><br>Carla<br><br><div class="gmail_quote">On Fri, Sep 3, 2010 at 10:35 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: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br><br>----- Original Message -----<br>From: Carla Jamous <<a href="mailto:carlajamous@gmail.com" target="_blank">carlajamous@gmail.com</a>><br>
Date: Friday, September 3, 2010 18:31<br>Subject: Re: [gmx-users] incomplete frame<br>To: <a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>, Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Thank you Justin for your advice,<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I did gmxcheck on the non-concatenated trajectory and found that my trajectory is not corrupted.<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I did re-run trjcat, without any problem. But when I run trjconv, it gives the same error message as before.<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> It's really strange because I'm sure that my trajectory is ok (with gmxcheck)!<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Please do you have another idea?<br><br></div>Have you run out of disk space, or run into a 2GB file size limit?<br>
<font color="#888888"><br>Mark</font><div><div></div><div class="h5"><br><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Thanks,<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Carla<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<div class="gmail_quote"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>On Thu, Sep 2, 2010 at 3:07 PM, Justin A. Lemkul <span dir="ltr"><<a>jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Carla Jamous wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Hi everyone,<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> I concatenated many trajectories with trjcat and didn't have any problem.<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> But when I did trjconv, I had this warning:<br> <font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> WARNING: Incomplete frame: nr 6077 time 12154<br> <font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> so I tried to do gmxcheck on my concatenated .xtc and got :<br> <font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Reading frame 0 time 0.000 # Atoms 192409<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Precision 0.001 (nm)<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Reading frame 6000 time 12000.001 WARNING: Incomplete frame: nr 6077 time 12154<br> <font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Item #frames Timestep (ps)<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Step 6077 2<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Time 6077 2<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Lambda 0<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Coords 6077 2<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Velocities 0<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Forces 0<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Box 6077 2<br> <font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> please can anyone tell me what might be the problem, knowing that when I gmxcheck the file .xtc that contains this frame, I don't get a warning.<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br> </blockquote> <font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
</div></div><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Two possibilities:<br> <font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> 1. trjcat corrupted the frame when trying to write the full trajectory<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> 2. The original non-concatenated trajectory is corrupted and trjcat passed over the problem, while trjconv cannot.<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Check the original (non-concatenated) trajectories to assess their integrity. If #1 is true, run trjcat again. If #2 is true, you cannot use the corrupted frame(s), which may mean re-running from a point prior to the corruption.<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> -Justin<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br> <blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Thank you,<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Carla<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br> </blockquote> <font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> -- <br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> ========================================<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Justin A. Lemkul<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Ph.D. Candidate<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> ICTAS Doctoral Scholar<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> MILES-IGERT Trainee<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Department of Biochemistry<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Virginia Tech<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Blacksburg, VA<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> ========================================<br>
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