Dear Justin: ------------------------- Program mdrun_d, VERSION 4.0.4 Source code file: gmx_fft_mkl.c, line: 825
Fatal error: Error executing Intel MKL FFT. ------------------------------------------------------- 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? 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? Anyone had the same problem before? On Fri, May 8, 2009 at 1:04 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Yanmei Song wrote: > >> Dear Justin: >> >> Sorry to bother so many times. After EM everything looks fine. However the >> mdrun died with the error: >> >> ------------------------------------------------------- >> Program mdrun_d, VERSION 4.0.4 >> Source code file: gmx_fft_mkl.c, line: 825 >> >> Fatal error: >> Error executing Intel MKL FFT. >> ------------------------------------------------------- >> >> what is the problem coming from? >> >> > 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. > > -Justin > > On Fri, May 8, 2009 at 11:28 AM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> VMD guesses bonds based on distances, so it is not necessarily very >> smart. >> >> 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. >> >> But in any case, bonds aren't broken and/or formed in classical MD >> so there is likely nothing to be concerned about. >> >> -Justin >> >> Yanmei Song wrote: >> >> Dear Justin: >> >> Thanks for your message. >> >> When I open the gro file using VMD it shows: >> >> atom:1950 >> bonds 1907 >> residue:43 >> >> I was thinking the problem may not come from the artifact of >> visualization. Since if the gro file is fine it should be like: >> >> atom:1950 >> bonds 1944 >> residue:6 >> >> because I have 6 chains in the box. >> >> This morning I found that it seems the problem was resolved by >> increasing the box size. Why is that? >> >> >> On Thu, May 7, 2009 at 5:10 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> Yanmei Song wrote: >> >> Dear users: >> >> 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. >> >> Steepest Descents converged to machine precision in 1545 >> steps, >> but did not reach the requested Fmax < 10. >> Potential Energy = -7.51461594735782e+03 >> Maximum force = 2.66505909651672e+02 on atom 1256 >> Norm of force = 9.84300153087768e+00 >> >> Anyone knows how to solve the problem? Thanks in advance! >> >> >> Probably an artifact of visualization, or otherwise periodic >> boundary conditions: >> >> http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions >> >> -Justin >> >> -- Yanmei Song >> Department of Chemical Engineering >> ASU >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org >> >> >> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search >> before posting! >> Please don't post (un)subscribe requests to the list. Use >> the >> www interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- Yanmei Song >> Department of Chemical Engineering >> ASU >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- >> Yanmei Song >> Department of Chemical Engineering >> ASU >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- Yanmei Song Department of Chemical Engineering ASU
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