<div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Apr 27, 2012 at 4:38 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
<br>
On 4/27/12 11:34 AM, Steven Neumann wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
<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></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 11:22 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 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>
</div></blockquote>
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If you need to change the .mdp file, you can't use tpbconv; use grompp to generate a new .tpr file and submit the new job. </blockquote><div><br>So if I will create new mdp file (with additional nstvout=0 to get rid of trr files) and use:<br>
<br>mdrun -s new.tpr -cpi last.cpt<br><br>Will I continue from the checkpoint? <br><br> </div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"> I'm not sure if you can pick up using mdrun -cpi if the settings have changed, but you can try.<span class="HOEnZb"><font color="#888888"><br>
</font></span></blockquote><div><br>Yes you can, from 4.0 you do not have to specify -append just -cpi file if the job crashed.<br><br> <br></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<span class="HOEnZb"><font color="#888888">
-Justin</font></span><div class="HOEnZb"><div class="h5"><br>
<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" value="+15402319080" target="_blank">(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>
<br>
==============================<u></u>==========<br>
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