Hi Blaise,<br><br>You'd better look in the log file where this starts. I bet it's either Lys-NH3+ or phosphate (ATP?) spinning like crazy. Check the archive for solutions.<br><br>Best,<br><br>Tsjerk<br><br><div><span class="gmail_quote">
On 10/2/07, <b class="gmail_sendername">Blaise Mathias-Costa</b> <<a href="mailto:bmathiascosta@unmc.edu">bmathiascosta@unmc.edu</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2"></font><div><div style="direction: ltr;"><font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">Hi all,<br><br>The mdrun stopped after
2.6nS after writing this error:<br>Step 1321571, time 2643.14 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>max 2.814066 (between atoms 2742 and 2745) rms 0.041434<br>bonds that rotated more than 30 degrees:
<br> atom 1 atom 2 angle previous, current, constraint length<br> 2742 2743 90.1 0.1728 0.0946 0.1000<br> 2742 2744 90.0 0.1010 0.2410 0.1000<br> 2742 2745 90.0 0.1675 0.3814
0.1000<br><br>like this for 100s of times..<br><br>here is the md.mdp file:<br>cpp = cpp<br>include = -I../top<br>define =<br>integrator = md<br>dt =
0.002<br>comm_grps = Protein<br>nstcomm = 1<br>nsteps = 2500000<br>nstxout = 5000<br>nstvout = 5000<br>nstlog = 5000<br>nstenergy = 500
<br>nstxtcout = 250<br>xtc_grps = Protein<br>energygrps = Protein non-protein<br>nstlist = 10<br></font></div><font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">
<span class="sg"><div> </div><div><br><div>Blaise Mathias Costa, PhD<br>Department of Pharmacology and Experimental Neuroscience<br>University of Nebraska Medical Center<br>Omaha, NE 68198-5800, USA.<br>Tel: 001 402 559 7132
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