Dear Justin:<br><br><div class="im">-------------------------<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>
-------------------------------------------------------</div><br>I really could not find out what is the reason for the error above. Do you mean something is wrong with the installation. if this is the case then should I re-install it?<br>
<br>This morning I did the same procedure with the same input file using gromacs-3.3.3 ( which means I did all the editconf, genbox EM, and mdrun in 3.3.3) and the mdrun works well. So I think there must be something wrong with the 4.0.4. How can I fix this?<br>
<br>Anyone had the same problem before? <br><br><br><br><div class="gmail_quote">On Fri, May 8, 2009 at 1:04 PM, 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>
<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 Justin:<br>
<br><div class="im">
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></blockquote>
<br>
It looks like you have Intel MKL for your FFT package, but mdrun can't find it (or it otherwise failed for some reason). Make sure your environment can find the location of all necessary binaries or libraries and try again.<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><div></div><div class="h5">
On Fri, May 8, 2009 at 11:28 AM, 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>
VMD guesses bonds based on distances, so it is not necessarily very<br>
smart.<br>
<br>
I have no idea why increasing the box causes the molecules to be<br>
displayed correctly, other than that VMD cannot deal with the<br>
periodicity correctly, as I implied before. Causing all of the<br>
molecules to be within the unit cell may lead VMD to induce the<br>
desired visualization.<br>
<br>
But in any case, bonds aren't broken and/or formed in classical MD<br>
so there is likely nothing to be concerned about.<br>
<br>
-Justin<br>
<br>
Yanmei Song wrote:<br>
<br>
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<br>
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<br>
increasing the box size. Why is that?<br>
<br>
<br>
On Thu, May 7, 2009 at 5:10 PM, Justin A. Lemkul<br>
<<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>><br></div></div><div><div></div><div class="h5">
<mailto:<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.<br>
After EM,<br>
there is no error message. However I found that in the<br>
gro file<br>
by visualization, 2 of the chains has been split in many<br>
parts,<br>
which means many bonds in the molecules disconnected. And<br>
also<br>
the other 4 are good. I checked em.log and eveyting looks<br>
fine.<br>
<br>
Steepest Descents converged to machine precision in 1545<br>
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>
------------------------------------------------------------------------<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>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540)<div class="im">
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<br>
-- Yanmei Song<br>
Department of Chemical Engineering<br>
ASU<br>
<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> <<a href="http://vt.edu" target="_blank">http://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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<br>
-- <br>
Yanmei Song<br>
Department of Chemical Engineering<br>
ASU<br>
</div></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>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Yanmei Song<br>Department of Chemical Engineering<br>ASU<br>