probably a bad starting structure...<br>check this website for pressure scaling warning : <a href="http://wiki.gromacs.org/index.php/Errors">http://wiki.gromacs.org/index.php/Errors</a><br><br>regards,<br>pawan<br><br><div class="gmail_quote">
On Mon, Apr 27, 2009 at 5:21 PM, Sheetal Arora <span dir="ltr"><<a href="mailto:sheetal.arora83@gmail.com">sheetal.arora83@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I am trying to run the simulation of protein ligand complex.<br>But after running the mdrun by giving command-"grompp –f md. mdp –c pr.gro –p trp.top –o md.tpr "<br>and then "nohup mdrun –deffnm md & "<br>
the md.log file is showing the following message-<br>Step 11 Warning: pressure scaling more than 1%, mu: 1.01684 1.01684 1.01684<br><br>Step 13 Warning: pressure scaling more than 1%, mu: 0.947161 0.947161 0.947161<br>
<br>Step 14 Warning: pressure scaling more than 1%, mu: 1.01207 1.01207 1.01207<br><br>Step 15 Warning: pressure scaling more than 1%, mu: 1.18248 1.18248 1.18248<br><br>Step 16 Warning: pressure scaling more than 1%, mu: 0.867467 0.867467 0.867467<br>
<br>Step 16, time 0.032 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>max 0.099556 (between atoms 1396 and 1398) rms 0.028595<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br>
21 23 30.8 0.1740 0.1569 0.1470<br> 38 40 32.0 0.1740 0.1583 0.1470<br> 54 56 33.0 0.1740 0.1588 0.1470<br> 56 57 30.6 0.1810 0.1623 0.1530<br>
67 69 31.4 0.1740 0.1568 0.1470<br> 104 106 32.6 0.1740 0.1588 0.1470<br> 106 107 31.1 0.1811 0.1632 0.1530<br> 216 218 31.8 0.1741 0.1584 0.1470<br>
I am attaching my md.mdp file.Please help me in this regard.<br clear="all"><font color="#888888"><br>-- <br>Sheetal Arora<br>M.Tech(Biotechnology & Medical Engg)<br><br>NIT Rourkela<br>
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