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 <jalem...@vt.edu
<mailto: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>
<mailto: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>>
<mailto: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
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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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