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

[Yanmei Song]

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> 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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>>
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>
> --
> ========================================
>
> 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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