<br><br><div class="gmail_quote">On Wed, Dec 15, 2010 at 12:53 AM, YUVRAJ UBOVEJA <span dir="ltr"><<a href="mailto:yuvrajthedon@gmail.com">yuvrajthedon@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hello<br><br>I am trying to simulate lipase in water in ffamber99sb-ildn. Chosen "cubic" as box with distance of 1nm b/w solute n box.<br>Protein is going out of the box after equilibration step. Any solution?<br>
<br></blockquote><div><br></div><div>The protein does not diffuse out of the box. Use for eg: trjconv -pbc nojump on your trajectory. For more information refer to the link below...</div><div><br></div><div><br></div><div>
<a href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</a></div><div><br></div><div><br></div><div>Best Wishes,</div>
<div><br></div><div><br></div><div>Sarath</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Should i use <b>freezegrps</b> option to restrict protein movement. Please provide some light to this option. What effect it will have on the whole system?<br clear="all">
<br>-- <br><font color="#888888">Yuvraj <br><br>
</font><br>--<br>
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