On Mon, Dec 10, 2012 at 9:48 PM, francesco oteri <francesco.ot...@gmail.com>wrote:
> Dear gromacs users, > > I am facing a very tricky problem in building a stable topology. > In particular I am trying to use MARTINI force-field and I noticed that if > I use a box whose the side size is smaller than 20nm, the minimization > fails with this message: > > Reading file 01em.tpr, VERSION 4.6-beta1 (single precision) > Starting 12 tMPI threads > Using 12 MPI threads > Making 2D domain decomposition 4 x 3 x 1 > > Steepest Descents: > Tolerance (Fmax) = 1.00000e+03 > Number of steps = 2000 > Step= 14, Dmax= 1.2e-06 nm, Epot= 4.42099e+18 Fmax= inf, atom= 39063 > Energy minimization has stopped, but the forces havenot converged to the > requested precision Fmax < 1000 (whichmay not be possible for your system). > It stoppedbecause the algorithm tried to make a new step whose sizewas too > small, or there was no change in the energy sincelast step. Either way, we > regard the minimization asconverged to within the available machine > precision,given your starting configuration and EM parameters. > > Double precision normally gives you higher accuracy, butthis is often not > needed for preparing to run moleculardynamics. > 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 15 steps, > but did not reach the requested Fmax < 1000. > Potential Energy = 4.4209897e+18 > Maximum force = inf on atom 39063 > Norm of force = inf > > gcq#142: "One Ripple At a Time" (Bianca's Smut Shack) > > But, if I use a box bigger then 19.5nm the minimization, although with some > LINCS warning, succeeded! > The standard advice here http://www.gromacs.org/Documentation/Terminology/Blowing_Up seems to apply, because your system also has problems with 4.5.5 and even when it "succeeds" there is evidence that something is not right (from the LINCS warnings) > I found the problem with gromacs 4.5.5, 4.6beta1 and beta2. > > I am attaching the script (crea_topo.csh) I am using to build the > topologies as well as all the input files you need to replicate the error. > > The different topologies have been obtained changing the value of the > variable side in crea_topo.csh > > As you can notice from the script, the structure is initially minimized in > vacuo to remove problems due in the all atoms-coarse grained transformation > and then it is solvated, Then, water molecules closer then 0.8nm to protein > are rmoved through vmd. > > Can you give me some clue on how to solve the problem, except changing the > software?. > As the above link suggests, make sure you visualize your results. Probably you will find an ion in an inappropriate place. > > I mean, I would like to know whether there is a bug or not in some of the > program used to build the topology. > genion can insert ions of arbitrary name and update the topology in one step. You don't need your second round of vmd or as much awking. genbox can do similarly - I'm surprised there's not an existing Martini workflow that uses genbox -vdwd 0.4 or similar to pre-exclude those waters. Neither of these is likely your problem, however. Mark > Francesco > > > 01em.mdp < > https://docs.google.com/file/d/0B1ktZ-u2OHFAejUwY2tnQnlnc3c/edit> > > crea_topo.csh< > https://docs.google.com/file/d/0B1ktZ-u2OHFAcHVZWXJCeXVBc3c/edit> > > Desu_OK.pdb< > https://docs.google.com/file/d/0B1ktZ-u2OHFAMkRScXlWYWlzMmc/edit> > > dsspcmbi < > https://docs.google.com/file/d/0B1ktZ-u2OHFAT2hCWVpGWDAwdEU/edit> > > ions.itp < > https://docs.google.com/file/d/0B1ktZ-u2OHFAYWdpa3o3N09sdEU/edit> > > martini.itp< > https://docs.google.com/file/d/0B1ktZ-u2OHFAOFVZNkwzN2J3c3c/edit> > > martinize.py< > https://docs.google.com/file/d/0B1ktZ-u2OHFAZ3hzWnZGcEJyTWM/edit> > > water-1bar-303K.gro< > https://docs.google.com/file/d/0B1ktZ-u2OHFAcmhMUS1YZEVlUjQ/edit> > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
