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<div class="gmail_quote">On Fri, Apr 27, 2012 at 5:13 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
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<div class="im"><br><br>On 4/27/12 12:09 PM, Steven Neumann wrote:<br></div>
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<div class="im"><br><br>On Fri, Apr 27, 2012 at 4:38 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div>
<div class="im"><mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br><br><br><br> On 4/27/12 11:34 AM, Steven Neumann wrote:<br><br><br><br> On Fri, Apr 27, 2012 at 4:28 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br></div>
<div>
<div class="h5"> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br><br><br><br> On 4/27/12 11:22 AM, Steven Neumann wrote:<br>
<br> Dear Gmx Users,<br><br> I am running 2 us simulation in implicit solvent model:<br><br> define = -DPOSRES<br> integrator = sd ; leap-frog integrator<br>
nsteps = 500000000 ; 0.004 * 500000000= 2 us<br> dt = 0.004 ; 4 fs<br> ; Output control<br> nstxout = 0<br> nstxtcout = 50000 ; xtc compressed trajectory output<br>
every 2 ps<br> nstenergy = 10000 ; save energies every 2 ps<br> nstlog = 10000 ; update log file every 2 ps<br><br> How come my trajectory (trr) is being created and takes 80 GB?<br>
<br><br> The default for nstvout is 100, so you're likely getting very frequent<br> output of velocities into the .trr file.<br><br> -Justin<br><br> Thank you<br> This job crashed due to the quota exceeded. If change my mdp file (with<br>
additional nstvout=0) using tpbconv and run it from the checkpoint file it<br> should work then with no trr file?<br><br><br> If you need to change the .mdp file, you can't use tpbconv; use grompp to<br>
generate a new .tpr file and submit the new job.<br><br><br>So if I will create new mdp file (with additional nstvout=0 to get rid of trr<br>files) and use:<br><br>mdrun -s new.tpr -cpi last.cpt<br><br>Will I continue from the checkpoint?<br>
<br></div></div></blockquote><br>That's the question I posed below...
<div class="im"><br><br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote"> I'm not sure if you can pick up using mdrun -cpi if the settings have<br> changed, but you can try.<br>
<br><br>Yes you can, from 4.0 you do not have to specify -append just -cpi file if the<br>job crashed.<br><br></blockquote><br></div>I am aware of checkpointing, but what I'm not sure of is if you change output options (or others) mid-stream, if the checkpointing mechanism will complain, particularly due to the changes in the .trr content. You'll have to try and see.
<div class="HOEnZb">
<div class="h5"><br><br>-Justin<br></div></div></blockquote>
<div> </div>
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<div>Indeed, it complains in terms of not present trr file (3 out of 4 files present) and he does not want to carry on. But when I change name of the output it starts from the checkpoint generating new files. Can I then somehow connect those two xtc trajectories using trjconv? Which tpr file I should use?</div>
<div> </div>
<div>Steven</div>
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<div class="HOEnZb">
<div class="h5"><br>-- <br>==============================<u></u>==========<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 href="http://vt.edu/" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" target="_blank" value="+15402319080">(540) 231-9080</a><br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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