[gmx-users] Subject: Molecule is breaking during energy minimization

[Emine Deniz Tekin]

Thanks for your quick reply.
Deniz

On Sun, Dec 11, 2016 at 3:44 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Almost certainly you are simply seeing a visualization artefact of
> http://www.gromacs.org/Documentation/Terminology/
> Periodic_Boundary_Conditions.
>
> Mark
>
> On Sun, Dec 11, 2016 at 10:02 PM Emine Deniz Tekin <edeniztekin at gmail.com>
> wrote:
>
>> Hi All,
>>
>>
>> I have 2 different Peptide Amphiphile molecules (say PA1 and PA2). Using
>> these two, I created a fiber structure. After 50.000 steps of energy
>> minimization simulation, which normally terminated, some residues of some
>> of the PA molecules broke away (I saw this disintegration with VMD).
>>
>>
>> To understand the possible reasons of disintegration, I have done two more
>> things:
>>
>>
>> 1- To check the accuracy of topology, I have also done energy minimization
>> of randomly distributed molecules (PA1 and PA2) and observed that there
>> was
>> no disintegration, all molecules were appearing normal.
>>
>>
>> 2- There may be a coordinate clash; I prepared several different fiber
>> structures (changing the angle between the PA molecules). But, in this
>> case, some parts of the fiber still broke away.
>>
>>
>> So at this point, I am not sure about the reason of disintegration at the
>> end of energy minimization.  I would appreciate any help. Thank you.
>>
>>
>>
>> Best regards,
>>
>> Deniz
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>