Hi, pdb2gmx and grompp are pretty talkative about things like missing parameters and bonds - go back and read what they had to say, and particularly what pdb2gmx thought about your specbonds.
Mark On Fri, Oct 23, 2015 at 5:51 PM faride badalkhani <farideh.kham...@gmail.com> wrote: > Hi, > > Thanks a lot for your time and patience. This time, I chose a very simple > structure and then inspected the generated topology. The interesting point > was that, there were some missing interactions. When I inspected them. I > found that I had defined those interactions in ffbonded.itp file, but > pdb2gmx has not assigned those definitions to these interactions. However, > I added the appropriate gb_, ga_, or gd_ manually, and then performed the > MD simulations and received an error as follows: > > Step= 210, Dmax= 6.6e-03 nm, Epot= -8.80977e+04 Fmax= 1.48278e+05, atom= > 46 > Step= 212, Dmax= 4.0e-03 nm, Epot= -8.90453e+04 Fmax= 1.76644e+05, atom= > 44 > Step= 216, Dmax= 5.9e-04 nm, Epot= -8.90760e+04 Fmax= 1.48643e+05, atom= > 46 > Step= 218, Dmax= 3.6e-04 nm, Epot= -8.91295e+04 Fmax= 1.75349e+05, atom= > 44 > Step= 221, Dmax= 1.1e-04 nm, Epot= -8.91493e+04 Fmax= 1.48437e+05, atom= > 46 > Step= 224, Dmax= 3.2e-05 nm, Epot= -8.91556e+04 Fmax= 1.74146e+05, atom= > 44 > Step= 227, Dmax= 9.6e-06 nm, Epot= -8.91559e+04 Fmax= 1.51118e+05, atom= > 46 > Step= 229, Dmax= 5.8e-06 nm, Epot= -8.91570e+04 Fmax= 1.71312e+05, atom= > 44 > Step= 232, Dmax= 1.7e-06 nm, Epot= -8.91571e+04 Fmax= 1.54271e+05, atom= > 46 > Step= 234, Dmax= 1.0e-06 nm, Epot= -8.91572e+04 Fmax= 1.70893e+05, atom= > 44 > Step= 235, Dmax= 1.2e-06 nm, Epot= -8.91570e+04 Fmax= 1.57473e+05, atom= > 46 > Energy minimization has stopped, but the forces have not converged to the > requested precision Fmax < 100 (which may not be possible for your system). > It stopped because the algorithm tried to make a new step whose size was > too > small, or there was no change in the energy since last step. Either way, we > regard the minimization as converged to within the available machine > precision, given your starting configuration and EM parameters. > > Double precision normally gives you higher accuracy, but this is often not > needed for preparing to run molecular dynamics. > You might need to increase your constraint accuracy, or turn > off constraints altogether (set constraints = none in mdp file) > > writing lowest energy coordinates. > > Steepest Descents converged to machine precision in 236 steps, > but did not reach the requested Fmax < 100. > Potential Energy = -8.9157188e+04 > Maximum force = 1.7089320e+05 on atom 44 > Norm of force = 3.3110510e+03 > > gcq#220: "Let's Go Hang Out In a Mall" (LIVE) > > farideh@farideh-P61A-D3:~/multiple/G0$ > > you can access all the files via the following link: > https://www.dropbox.com/s/m1kxafyu1n749hb/G0.zip?dl=0 > > Truly yours, > Farideh > > On Thu, Oct 22, 2015 at 11:24 AM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > > > 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. > > > -- > 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.