Hi, 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 them.
Mark On Thu, Oct 22, 2015 at 9:35 AM faride badalkhani <farideh.kham...@gmail.com> wrote: > 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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.