<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#FFFFFF">
On 21/11/2011 9:02 PM, Vasileios Tatsis wrote:
<blockquote
cite="mid:1321869731.91864.YahooMailNeo@web26706.mail.ukl.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: verdana,helvetica,sans-serif; font-size:
12pt;">
<div>Dear Gromacs Users,</div>
<div><br>
</div>
<div>The following error messages appear while running MD
simulations with Gromacs 4.5.4: <br>
</div>
<div><br>
</div>
<div>- Cannot flush logfile - maybe you are out of quota?</div>
<div>- XTC error - maybe you are out of quota?</div>
<div>- Cannot read/write checkpoint; corrupt file, or maybe you
are out of quota?</div>
<div>- Cannot write trajectory frame; maybe you are out of
quota?</div>
</div>
</blockquote>
<br>
GROMACS is having trouble writing a file when it wants to. In the
absence of further clues, I think your (network?) file system has
some issues. Check you have write permission for the directory into
which you are writing.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:1321869731.91864.YahooMailNeo@web26706.mail.ukl.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff;
font-family:verdana, helvetica, sans-serif;font-size:12pt">
<div><br>
</div>
<div>I use the following parameters for the output files:</div>
<div><br>
</div>
<div>###################################<br>
</div>
<div>; Output control<br>
; frequency to write coordinates to output trajectory file<br>
nstxout = 1000<br>
; frequency to write velocities to output trajectory<br>
nstvout = 1000<br>
; frequency to write forces to output trajectory<br>
nstfout = 0<br>
; frequency to write energies to log file<br>
nstlog = 1000<br>
; frequency to write energies to energy file<br>
nstenergy = 1000<br>
; frequency to write coordinates to xtc trajectory<br>
nstxtcout = 1000<br>
; precision to write to xtc trajectory<br>
xtc-precision = 1000<br>
</div>
<div>###################################</div>
<div><br>
</div>
<div>Also, I have to note that I have compiled Gromacs 4.5.4
with openMPI 1.4.3.</div>
<div>The available disk space is more than 0.4 TB.<br>
</div>
<div><br>
</div>
<div>Thanks in advance for your help<br>
</div>
<div><br>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>