<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 style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">Select a group: 2<BR>Selected 2: 'Protein-H'<BR>trn version: GMX_trn_file (single precision)<BR>Reading frame 0 time 125.000</DIV>
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<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">'nuff said. Couldn't comment on the time between frames in your file. gmxdump will tell you, or get it from (nstxout or nstxtcout)*dt in your mdp.</DIV>
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<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">----- Original Message ----<BR>From: Liu Shiyong <liushiyong@gmail.com><BR>To: Discussion list for GROMACS users <gmx-users@gromacs.org><BR>Sent: Wednesday, March 12, 2008 11:24:00 PM<BR>Subject: Re: [gmx-users] trjconv output at a specified time<BR><BR>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" target=_blank rel=nofollow ymailto="mailto:anoddlad@yahoo.com">anoddlad@yahoo.com</A>> wrote:<BR>
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<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>
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<DIV class=Wj3C7c>----- Original Message ----<BR>From: Liu Shiyong <<A href="mailto:liushiyong@gmail.com" target=_blank rel=nofollow ymailto="mailto:liushiyong@gmail.com">liushiyong@gmail.com</A>><BR>To: Discussion list for GROMACS users <<A href="mailto:gmx-users@gromacs.org" target=_blank rel=nofollow ymailto="mailto:gmx-users@gromacs.org">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" target=_blank rel=nofollow ymailto="mailto:syliu@ku.edu">syliu@ku.edu</A> (<A href="mailto:shiyongliu@ku.edu" target=_blank rel=nofollow ymailto="mailto:shiyongliu@ku.edu">shiyongliu@ku.edu</A> or <A href="mailto:liushiyong@ku.edu" target=_blank rel=nofollow ymailto="mailto:liushiyong@ku.edu">liushiyong@ku.edu</A>)<BR>Homepage: <A href="http://www.people.ku.edu/~syliu" target=_blank rel=nofollow>http://www.people.ku.edu/~syliu</A><BR>Lab: <A
href="http://vakser.bioinformatics.ku.edu/people" target=_blank rel=nofollow>http://vakser.bioinformatics.ku.edu/people</A><BR>Phone: (785) 864-1962 </DIV></DIV>
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ymailto="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 rel=nofollow>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" target=_blank rel=nofollow ymailto="mailto:syliu@ku.edu">syliu@ku.edu</A> (<A href="mailto:shiyongliu@ku.edu" target=_blank rel=nofollow ymailto="mailto:shiyongliu@ku.edu">shiyongliu@ku.edu</A> or <A href="mailto:liushiyong@ku.edu" target=_blank rel=nofollow ymailto="mailto:liushiyong@ku.edu">liushiyong@ku.edu</A>)<BR>Homepage: <A href="http://www.people.ku.edu/~syliu" target=_blank rel=nofollow>http://www.people.ku.edu/~syliu</A><BR>Lab: <A href="http://vakser.bioinformatics.ku.edu/people" target=_blank
rel=nofollow>http://vakser.bioinformatics.ku.edu/people</A><BR>Phone: (785) 864-1962<!-- kill -->
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