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<DIV><FONT face=Arial size=2><FONT face="Times New Roman" size=3>>To whom it
concerns,<BR><FONT face=Arial size=2>></FONT><BR>>I am trying to run a
long time MD simulation on a complicated system<BR>>composed of two axt
molecules and two proteins with Gromacs. I set <BR><FONT face=Arial
size=2>></FONT><BR>>nstxtcout=100<BR>>nstxout=5000<BR>>nstvout=5000<BR>>dt=0.002<BR>>nsteps=500000<BR>>nstlog=200<BR>><BR>>in
the .mdp file to get the 1000ps result. But the real output result
is<BR>>only 110s. The size of the output file are:<BR>><BR>>.log
2147483647<BR>>.trr 13120992<BR>>.tpr
6588032<BR>><BR>>Is it because of the size limit of the output file?
what's the size<BR>>limit of all the output files? what should i do then? If
not, why I<BR>>cannot get the right long time run?<BR>><BR>>Thanks in
advance,<BR>><BR>>-- <BR>>xiaoyi li <</FONT><A
href="mailto:xiaoyi@xray.bmc.uu.se"><FONT face="Times New Roman"
size=3>xiaoyi@xray.bmc.uu.se</FONT></A><FONT face="Times New Roman"
size=3>></FONT><BR><FONT face="Times New Roman" size=3>></FONT><BR>Some
unix instalations has filesize limit of 2</FONT><FONT face=Arial size=2><FONT
face=Arial size=2>GB</FONT></FONT></DIV>
<DIV><FONT face=Arial size=2>so this could be the case.</FONT></DIV>
<DIV><FONT face=Arial size=2><FONT face="Times New Roman"
size=3>Check</FONT> filesize limit by</FONT></DIV>
<DIV><FONT face=Arial size=2>ulimit -f</FONT></DIV>
<DIV><FONT face=Arial size=2>(in bash, I don't know how to do this in other
shells).</FONT></DIV>
<DIV><FONT face=Arial size=2>if the answer is not "unlimited" </FONT><FONT
face=Arial size=2>type</FONT></DIV>
<DIV><FONT face=Arial size=2>ulimit -f unlimited</FONT></DIV>
<DIV><FONT face=Arial size=2>or call your clustermaster.</FONT></DIV>
<DIV><FONT face=Arial size=2>The precompiled version of gromacs could also
have</FONT></DIV>
<DIV><FONT face=Arial size=2>such limit. I had this problem with Gamess US
and I</FONT></DIV>
<DIV><FONT face=Arial size=2>fixed it by replacement of precompiled version
by</FONT></DIV>
<DIV><FONT face=Arial size=2>one that I compiled myself. Gromacs could also
crash</FONT></DIV>
<DIV><FONT face=Arial size=2>on Athlon without any reason (there are some
mails</FONT></DIV>
<DIV><FONT face=Arial size=2>dealing with this problem in GMX
archive).</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Vojtech Spiwok</FONT></DIV>
<DIV><FONT face=Arial size=2>ICT Prague</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
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