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 )? James 2013/1/1, Justin Lemkul <jalem...@vt.edu>: > > > On 1/1/13 2:01 PM, James Starlight wrote: >> Have someone else any ideas how the topology for a simple 2D lattice >> could be done ?:) >> >> I've tried to build it manually but for the system of 48 nodes >> definition of the angles and impropers have appeared very routinely :( >> > > For regularly spaced atoms, g_x2top should do it. > > -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
