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<DIV><FONT color=#000000 size=2 face=Arial>Dear gmxusers,</FONT></DIV>
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<DIV><FONT size=2 face=Arial>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:</FONT></DIV>
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<DIV dir=ltr>Program mdrun_mpi, VERSION 4.0.7<BR>Source code file: trnio.c, line: 252</DIV>
<DIV dir=ltr>File input/output error:<BR>Cannot write trajectory frame; maybe you are out of quota?</DIV>
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<DIV><FONT size=2 face=Arial>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. </FONT></DIV>
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<DIV><FONT size=2 face=Arial>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.</FONT></DIV>
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<DIV><FONT size=2 face=Arial>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<BR></FONT><FONT size=2 face=Arial></DIV></FONT>
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<DIV><FONT size=2 face=Arial>Many thanks for your help!</FONT></DIV>
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