Justin, so why my simulation of the sp3 lattice have been crashed with the links warnings ( which always tells about wrong geometry in topology)?
also I've tried to paraetrize completely planar (sp2) lattice but obtain errors like that Can not find forcefield for atom C27-22 with 2 bonds Can not find forcefield for atom C28-23 with 3 bonds Can not find forcefield for atom C4-24 with 3 bonds Can not find forcefield for atom C15-25 with 3 bonds Can not find forcefield for atom C1-26 with 3 bonds Can not find forcefield for atom C39-27 with 3 bonds Can not find forcefield for atom C41-28 with 3 bonds Can not find forcefield for atom C30-29 with 3 bonds Can not find forcefield for atom C2-30 with 2 bonds Can not find forcefield for atom C5-31 with 2 bonds Can not find forcefield for atom C8-32 with 3 bonds Can not find forcefield for atom H22-33 with 0 bonds So I've decided that the atom names is also relevant besides the geometry which was correct in that case. James 2013/1/2, Justin Lemkul <jalem...@vt.edu>: > > > On 1/2/13 4:36 AM, James Starlight wrote: >> Justin, >> >> >> I've already tried use g_x2top for the model of the system built from >> regularly spaced C-atoms ( with included hydrogens to specify sp3 >> hybridization). >> >> By means of that command I've created topology for my lattice with big >> force constant ( for the simulation of the very rigid structure) >> >> g_x2top -f lattice_h.pdb -o lattice.top -ff oplsaa -kb 500000 -kt 4000 >> -kp 500 -remdih >> >> >> the main problem which I've forced is the the absence of >> automate-generated impropers. As the result my lattice model at the >> beginning of the simulation (langevin's dynamics, nvt) have been >> perturbed and simulation finished with alot of lincs warnings. How I >> oculd fix it ? Should I use another atom names in the initial model ( >> e.g from polar hydrogens )? >> > > A bunch of sp3 carbons with attached hydrogens will not have any impropers, > > because the carbon centers are not planar. Atom names are irrelevant; > g_x2top > will do what you tell it based on bonded geometry. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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
