[gmx-users] Some molecules disconnected into many parts after EM
Yanmei Song
ysong30 at asu.edu
Mon May 11 21:49:20 CEST 2009
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 <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>> 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>>> 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> | (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
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
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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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
--
Yanmei Song
Department of Chemical Engineering
ASU
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