Dear Justin:<br><br>Thanks for your message. <br><br>When I open the gro file using VMD it shows: <br><br>atom:1950<br>bonds 1907<br>residue:43<br><br>I was thinking the problem may not come from the artifact of visualization. Since if the gro file is fine it should be like:<br>
<br>atom:1950<br>
bonds 1944<br>
residue:6<br><br>because I have 6 chains in the box.<br><br>This morning I found that it seems the problem was resolved by increasing the box size. Why is that? <br><br><br><div class="gmail_quote">On Thu, May 7, 2009 at 5:10 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
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<div><div></div><div><br>
<br>
Yanmei Song 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 users:<br>
<br>
I set up a 8nm cubic box with 6 long chain molecules. After EM, there is no error message. However I found that in the gro file by visualization, 2 of the chains has been split in many parts, which means many bonds in the molecules disconnected. And also the other 4 are good. I checked em.log and eveyting looks fine.<br>
<br>
Steepest Descents converged to machine precision in 1545 steps,<br>
but did not reach the requested Fmax < 10.<br>
Potential Energy = -7.51461594735782e+03<br>
Maximum force = 2.66505909651672e+02 on atom 1256<br>
Norm of force = 9.84300153087768e+00<br>
<br>
Anyone knows how to solve the problem? Thanks in advance!<br>
<br>
</blockquote>
<br></div></div>
Probably an artifact of visualization, or otherwise periodic boundary conditions:<br>
<br>
<a href="http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions" target="_blank">http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions</a><br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>
-- <br>
Yanmei Song<br>
Department of Chemical Engineering<br>
ASU<br>
<br>
<br></div>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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</blockquote></div><br><br clear="all"><br>-- <br>Yanmei Song<br>Department of Chemical Engineering<br>ASU<br>