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

[Mark Abraham]

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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