<div dir="ltr">I think system is not properly minimized. Try minimizing it first using l-bfgs (very helpful in these cases) followed by steep or conj. Make sure you are getting unrestrained minimization before running MD simulation. <br>
<br><div class="gmail_quote">On Mon, Sep 15, 2008 at 11:13 AM, Morteza Khabiri <span dir="ltr"><<a href="mailto:khabiri@greentech.cz">khabiri@greentech.cz</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;">
Dear gmxuser<br>
<br>
Thanks for your advices. Because of your help I could run my solution and<br>
protein together.<br>
but during the run I faced with this warning which cause the run again be<br>
crashed, The message is:<br>
<br>
relative constraint deviation after LINCS:<br>
max 0.000615 (between atoms 1731 and 1732) rms 0.000023<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
1731 1732 30.7 0.1000 0.0999 0.1000<br>
<br>
do anybody knows what should I do now?<br>
<br>
Thanks<br>
<br>
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</blockquote></div><br></div>