[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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