[gmx-users] energy minimization error

Mark Abraham mark.j.abraham at gmail.com
Thu Oct 22 09:54:13 CEST 2015


Did you inspect your topology like I suggested? You need to know that there
are bonds exactly where you intend them, before doing any calculations with


On Thu, Oct 22, 2015 at 9:35 AM faride badalkhani <farideh.khamseh at gmail.com>

> Hi,
> 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:
> https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0
> 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
> Farideh
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