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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Hi guys<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Thanks for your help! I will consider your suggestions.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Huiwen<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
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<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> NG HUI WEN <br>
<b>Sent:</b> Monday, August 09, 2010 11:05 AM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> Large output files and limited disk space. How do I handle
them?<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'>Dear gmxusers,</span><o:p></o:p></p>
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<p class=MsoNormal> <o:p></o:p></p>
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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>I
have a very basic question here which I hope someone could help me with. I was
running a couple of simulations over the weekend on a shared cluster and both
came to a stop for the same reasons:</span><o:p></o:p></p>
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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> <o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Program
mdrun_mpi, VERSION 4.0.7<br>
Source code file: trnio.c, line: 252<o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>File
input/output error:<br>
Cannot write trajectory frame; maybe you are out of quota?<o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> <o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Indeed there
were quite a number of large files in my user directory (e.g.
the .trr files and etc). I think the problems probably arise
from the fact that (i) I am storing my trajectory as full precision .trr
files and (ii) setting too small a value for nstxout and nstvout
in .mdp. </span><o:p></o:p></p>
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<p class=MsoNormal> <o:p></o:p></p>
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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>I
have seen some tutorials that suggested using "trjconv" to derive the
reduced precision .xtc files from the .trr files and then discard the
latter. My question is, would this be wise as I am not sure whether I
would find myself needing these .trr files in the future.</span><o:p></o:p></p>
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<p class=MsoNormal> <o:p></o:p></p>
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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Here's
a snippet of my .mdp file. Am I saving my coordinates and velocities too
frequently? If I were to increase this, are there any compelling factors that I
need to take into considerations?<br>
; Run parameters<br>
integrator =
md ;
leap-frog integrator<br>
nsteps =
500000 ; 2 * 500000 = 1000 ps (1 ns)<br>
dt
= 0.002 ; 2 fs<br>
; Output control<br>
nstxout =
100 ; save
coordinates every 0.2 ps<br>
nstvout =
100 ; save
velocities every 0.2 ps<br>
nstenergy =
100 ; save energies
every 0.2 ps<br>
nstlog =
100 ; update log
file every 0.2 ps<o:p></o:p></span></p>
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<p class=MsoNormal> <o:p></o:p></p>
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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Many
thanks for your help!</span><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> <o:p></o:p></p>
</div>
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