Justin, I want to simulate lattice with flexible nodes ( to examine fluctuations of that system by mens of Normal Mode Analysis). If I choose sp3 carbons as the nodes I obtain such lattice. But In that system hydrogens are also present which are not desirable in my system ( i want system consisted of only one type of atoms). On contrary if I choose sp2 hydrogens as the nodes I obtain completely rigid lattice which are not suitable for me.
I suppose that united-atom model could be suitable for such flexible lattice but I've failed to apply g_x2top on my lattice with gromos force field ( I have no problems with the opls-aa for this system). Here I've obtain errors like Can not find forcefield for atom C116-70 with 3 bonds Can not find forcefield for atom C119-71 with 3 bonds Can not find forcefield for atom C120-72 with 3 bonds Can not find forcefield for atom C121-73 with 3 bonds Can not find forcefield for atom C122-74 with 3 bonds Can not find forcefield for atom C124-75 with 3 bonds Can not find forcefield for atom C125-76 with 3 bonds Can not find forcefield for atom C126-77 with 3 bonds Can not find forcefield for atom C127-78 with 3 bonds Can not find forcefield for atom H01-79 with 0 bonds Can not find forcefield for atom H02-80 with 0 bonds Can not find forcefield for atom H03-81 with 0 bonds Can not find forcefield for atom H04-82 with 0 bonds Can not find forcefield for atom H05-83 with 0 bonds So it seems that the bonds between C and H atoms were not recognized correclty in case of gromos-ff. Must the some corrections be done in the atomname2type.n2t file ? James 2013/1/2, Justin Lemkul <jalem...@vt.edu>: > > > On 1/2/13 3:08 PM, James Starlight wrote: >> Justin, >> >> I want to simulate flexible lattice consist of only one type of atoms >> (nodes). So the planar (sp2 ) carbons are rigid. On other hand more >> flexible (sp3) carbons connected with hydrogens but I want that >> hydrogens were not included in my lattice. Should I use another >> (what? )atom-type for the node of my lattice ? >> > > I'm sorry to say I don't understand what you're saying. If you want a > lattice > of carbon atoms, you can surely develop a united-atom model of such a > lattice > and never involve hydrogen atoms of any sort. Again, valence depends > entirely > upon what you define in the topology or its precursors (.n2t or .rtp). > > -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
