Dear Justin:<br><br>Sorry to bother so many times. After EM everything looks fine. However the mdrun died with the error:<br><br>-------------------------------------------------------<br>Program mdrun_d, VERSION 4.0.4<br>
Source code file: gmx_fft_mkl.c, line: 825<br><br>Fatal error:<br>Error executing Intel MKL FFT.<br>-------------------------------------------------------<br><br>what is the problem coming from? <br><br><div class="gmail_quote">
On Fri, May 8, 2009 at 11:28 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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;">
<br>
VMD guesses bonds based on distances, so it is not necessarily very smart.<br>
<br>
I have no idea why increasing the box causes the molecules to be displayed correctly, other than that VMD cannot deal with the periodicity correctly, as I implied before. Causing all of the molecules to be within the unit cell may lead VMD to induce the desired visualization.<br>
<br>
But in any case, bonds aren't broken and/or formed in classical MD so there is likely nothing to be concerned about.<br>
<br>
-Justin<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;"><div class="im">
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><div class="im">
On Thu, May 7, 2009 at 5:10 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Yanmei Song wrote:<br>
<br>
Dear users:<br>
<br>
I set up a 8nm cubic box with 6 long chain molecules. After EM,<br>
there is no error message. However I found that in the gro file<br>
by visualization, 2 of the chains has been split in many parts,<br>
which means many bonds in the molecules disconnected. And also<br>
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>
<br>
Probably an artifact of visualization, or otherwise periodic<br>
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>
-- Yanmei Song<br>
Department of Chemical Engineering<br>
ASU<br>
<br>
<br>
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-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
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<br>
<br>
<br>
-- <br>
Yanmei Song<br>
Department of Chemical Engineering<br>
ASU<br>
</div></blockquote><div><div></div><div class="h5">
<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>
<br>
========================================<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Yanmei Song<br>Department of Chemical Engineering<br>ASU<br>