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

[Yanmei Song]

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?

On Fri, May 8, 2009 at 11:28 AM, Justin A. Lemkul <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>> 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> | (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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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>



-- 
Yanmei Song
Department of Chemical Engineering
ASU
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