[gmx-users] Some molecules disconnected into many parts after EM

Justin A. Lemkul jalemkul at vt.edu
Mon May 11 21:55:29 CEST 2009



Yanmei Song wrote:
> 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?
> 
> 

By default, your system configuration probably located Intel's MKL FFT package. 
  Likely your 3.3.3 installation was installed using something else, like FFTW. 
  I would recommend re-installing 4.0.4, using FFTW (if you have it), paying 
attention to the information that the ./configure step prints to the screen, and 
trying again.

-Justin

> 
> On Fri, May 8, 2009 at 1:04 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at 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
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at 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
>                <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at 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
> 
> 
>                            
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> 
>                   --    ========================================
> 
>                   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>
>         <http://vt.edu> | (540)
> 
>                231-9080
> 
>                   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 
> 
>                --        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> <http://vt.edu> | (540)
>         231-9080
>            http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 
> 
>         -- 
>         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
> 
>     ========================================
> 
> 
> 
> 
> -- 
> 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

========================================



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