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

[Emine Deniz Tekin]

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