Thanks.<br><br>The trajectory starts at 125ps ?<br><br>So step 1 == 125 ps <br> step 2 == 250 ps <br> step 3 == 375 ps <br><br>Where is 125ps from ?<br><br>But <br><br>; RUN CONTROL PARAMETERS<br>integrator = steep<br>
; Start time and timestep in ps<br>tinit = 0<br>dt = 0.002<br><br><br><br><div class="gmail_quote">On Wed, Mar 12, 2008 at 5:32 PM, Alan Dodd <<a href="mailto:anoddlad@yahoo.com">anoddlad@yahoo.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-size: 12pt; font-family: times new roman,new york,times,serif;">
You asked for the frame at 1ps. The trajectory starts at 125ps, so unsurprisingly the program does not give you an output.<br><br>
<div style="font-size: 12pt; font-family: times new roman,new york,times,serif;"><div><div></div><div class="Wj3C7c">----- Original Message ----<br>From: Liu Shiyong <<a href="mailto:liushiyong@gmail.com" target="_blank">liushiyong@gmail.com</a>><br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>Sent: Wednesday, March 12, 2008 10:07:17 PM<br>Subject: [gmx-users] trjconv output at a specified time<br>
<br>Hi, <br><br>I want to output a structure in a given time, for example , in step 1 during minimization.<br><br>I tried the following command using dump:<br>trjconv -f r-l_1_oplsaa.minim_traj.trr -timestep 1 -o m.pdb -s r-l_1_oplsaa.input.tpr -t0 0 -dump 1 <br clear="all">
<br>But It didnot work.<br><br>Output msg:<br><br>Select a group: 2<br>Selected 2: 'Protein-H'<br>trn version: GMX_trn_file (single precision)<br>Reading frame 0 time 125.000<br>Back Off! I just backed up m.pdb to
./#m.pdb.1#<br>Last frame 19 time 2418.000<br><br>WARNING no output, trajectory ended at 2418<br><br><br>gcq#76: "Baseball Heroes Only" (P.J. Harvey)<br><br>Best<br><br>-- <br>Shiyong Liu<br>Research Assistant<br>
center for bioinformatics in the university of kansas<br>Lab: (785)864-1962<br>Email: <a href="mailto:syliu@ku.edu" rel="nofollow" target="_blank">syliu@ku.edu</a> (<a href="mailto:shiyongliu@ku.edu" rel="nofollow" target="_blank">shiyongliu@ku.edu</a> or <a href="mailto:liushiyong@ku.edu" rel="nofollow" target="_blank">liushiyong@ku.edu</a>)<br>
Homepage: <a href="http://www.people.ku.edu/%7Esyliu" rel="nofollow" target="_blank">http://www.people.ku.edu/~syliu</a><br>Lab: <a href="http://vakser.bioinformatics.ku.edu/people" rel="nofollow" target="_blank">http://vakser.bioinformatics.ku.edu/people</a><br>
Phone: (785)
864-1962
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Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br><br clear="all"><br>-- <br>Shiyong Liu<br>Research Assistant<br>
center for bioinformatics in the university of kansas<br>Lab: (785)864-1962<br>Email: <a href="mailto:syliu@ku.edu">syliu@ku.edu</a> (<a href="mailto:shiyongliu@ku.edu">shiyongliu@ku.edu</a> or <a href="mailto:liushiyong@ku.edu">liushiyong@ku.edu</a>)<br>
Homepage: <a href="http://www.people.ku.edu/~syliu">http://www.people.ku.edu/~syliu</a><br>Lab: <a href="http://vakser.bioinformatics.ku.edu/people">http://vakser.bioinformatics.ku.edu/people</a><br>Phone:        (785) 864-1962