<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div>Hi Justin,</div><div> In many of the frames, if I use -b and -e to be same , it works</div><div>For example, I found if I use -b 16 -e 16, it gives me the the snapshot at 16ps. But, in many cases like 14ps, it is not working. Also, I tried <span class="Apple-style-span" style="font-family: arial, helvetica, sans-serif; font-size: 13px; ">-b 13 -e 14 -dump 14 . It does not work saying 'WARNING no output, trajectory ended at 14'</span></div><div>Any help will be appreciated.</div><div>Sanku</div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Justin A. Lemkul
<jalemkul@vt.edu><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Thu, May 5, 2011 10:22:38 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] trjconv problem<br></font><br>
<br><br>Sanku M wrote:<br>> Hi,<br>> I am having a problem with trjconv to get a single snap-shot from a trajectory file. I am using gromacs 4.0.7 .<br>> If I try to get a snapshot corresponding to 14 ps, I was trying to use "-b 14 -e 14 " command as follows. But,<br>> If I issue this command as shown below<br>> trjconv --f traj.xtc -o conf_pep.gro -s topol.tpr -b 14.0 -e 14.0 it crashes with following error:<br>> Precision of traj.xtc is 0.001 (nm)<br>> Using output precision of 0.001 (nm)<br>> <br>> WARNING no output, trajectory ended at 14<br>> <br>> However, if I issue the same trjconv command using "-dump 14" as shown below, trjconv provides the correct snapshot at 14 ps:<br>> trjconv --f traj.xtc -o conf_pep.gro -s topol.tpr -dump 14.0 But, this "-dump 14" command becomes extremely time consuming as I was trying to get the snap-shot for a long time i.e around
30000ps . So, I am trying to get "-b 14 -e 14" command work . So, I was wondering whether you have any clue how to get around with this.<br><br>If I recall, -b and -e cannot be the same. This is the reason for -dump. It might be worth a try to see if trjconv -b 13 -e 14 -dump 14 speeds things up any.<br><br>-Justin<br><br>> Sanku<br>> <br>> <br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a target="_blank" href="http://vt.edu">vt.edu</a> | (540) 231-9080<br><span><a target="_blank" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></span><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org"
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