[gmx-users] Subject: Molecule is breaking during energy minimization
mark.j.abraham at gmail.com
Sun Dec 11 13:44:31 CET 2016
Almost certainly you are simply seeing a visualization artefact of
On Sun, Dec 11, 2016 at 10:02 PM Emine Deniz Tekin <edeniztekin at gmail.com>
> 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
> 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,
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