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<DIV><FONT face=Arial size=2>Dear Colleagues,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I am trying to do the same procedure on my protein
containing a cofactor as described in the GROMACS Tutorial for Drug-Enzyme
complex (by John Kerringan). Things were going ok (as far as I can see) until I
tried to run MD of my system. i.e., issuing the following command:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>mdrun -s xxx.tpr -o xxx.trr -c xxx.gro</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>It goes few lines and after the following lines it
stops and doesn't go further. </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>
<DIV><FONT face=Arial size=2>atom1 atom2 angle previous, current, constraint
length</FONT></DIV>
<DIV><FONT face=Arial size=2>6446 6447
38.9 0.1080 0.1080
0.1080</FONT></DIV>
<DIV><FONT face=Arial size=2>9060 9061
90.0 0.1080 0.1650
0.1080</FONT></DIV>
<DIV><FONT face=Arial size=2>9840 9841
43.6 0.1080 0.1080
0.1080</FONT></DIV>
<DIV> </DIV></FONT></DIV>
<DIV><FONT face=Arial size=2>The CPU of the computer is almost fully engaged by
mdrun program, however it doesn't move further.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I know that it is hard to rectify such problem with
such a short description, however, I will appreciate it if you could kindly let
me know what is the problem.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Cheers,</FONT></DIV>
<DIV><FONT face=Arial size=2>Siavoush</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
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