Justin, yes, the main task is the parametrization of the simple 2D lattice which I created from sp3 carbons as the nodes. Now the main task is the reducing of that model to simplest 2D lattice made from 1 type of any atom connected with the 3 adjacent nodes via flexible bonds.
Might I define new atom type for that node in the atomname2type.n2t file placed to the work dir or should I add that atom to the ffbonded of the opls or gromos ff ? James 2013/1/3, Justin Lemkul <jalem...@vt.edu>: > > > On 1/3/13 2:46 AM, James Starlight wrote: >> 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. >> > > OK, so all the talk of a 2D lattice and issues assigning impropers really > wasn't > what you wanted after all? This whole thread has gotten to be very > meandering > and contradictory, I'm sorry to say. Only now after several days of posts > do > your real goals come out. > >> 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 ? >> > > There are no explicit hydrogens in any of the Gromos force fields for atoms > like > these (hence "united atom"), and IIRC there are no .n2t files for any of > them. > So it's not a matter of changing an .n2t file, it's a matter of creating > one. > > -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
