[gmx-users] energy minimization error

faride badalkhani farideh.khamseh at gmail.com
Thu Oct 22 09:34:50 CEST 2015


I am trying to simulate a hyper-branched polymer (a dendrimer) in water.
But, every time the system blows up at energy minimization step. Therefore,
according to what Mark had recommended I decided to start with a much
smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I had
optimized it at M062x/6-31G* level, before starting the MD simulations.
Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it
residue by residue. After that, I started simulation procedure and
continued step by step. In spite of G3 PAMAM dendrimer I didn't face any
errors in energy minimization step, and the potential energy - EM step plot
was reasonable. But, when I loaded em.gro file in VMD, the structure was
completely messed up as in G3 dendrimer. This time I continued the MD
simulation until production MD, and there was no error. However, the system
is blown up. You can access all the simulation files, pdb structure, and
the photos of G1 structure before and after EM step via:


Since I am a beginner in this area, I do not know what is the solution for
this problem.
Do you think errors that occur during the G3 simulation are relevant to the
initial structure?
any suggestion or recommendation is appreciated.

Thanks in advance

More information about the gromacs.org_gmx-users mailing list