Justin, thanks again for explanation. By the way if I define in topology top LJ params like
; Include forcefield parameters #include "gromos53a5.ff/forcefield.itp" [ atomtypes ] ;name at.num mass charge ptype c6 c12 CH2 6 0.000 0.000 A 0.0074684164 3.3965584e-05 CH3 6 0.000 0.000 A 0.0096138025 2.6646244e-05 [ nonbond_params ] ; i j func c6 c12 CH3 CH2 1 0.008473481 3.0084136e-05 [ moleculetype ] ; Name nrexcl ICE 3 i've obtain warns WARNING 1 [file lattice.top, line 23]: Overriding atomtype CH2 WARNING 2 [file lattice.top, line 24]: Overriding atomtype CH3 does it mean that the params from topology.top will be used instead of RTP file ? James 2013/1/3, Justin Lemkul <jalem...@vt.edu>: > > > On 1/3/13 11:49 AM, James Starlight wrote: >> Justin, >> >> >> I've made new lattice model in GROMOS united atoms. I've used 2 nodes >> - CH2 (ca) for atom with 3 bonds as well as CH1 (CB) for boundary >> atoms with 2 bonds to adjacent nodes. > > I'm assuming you've simply switched the atom types here. A CH2 should not > have > 3 other bonds. > >> That system is considerably rigid in comparison to the lattice which >> I've simulated in OPLS all atom ff. >> >> Does it possible to change VDW(LJ) parameters for both nodes in the >> top file or should I modify existing atom types in ffnonbonded ? >> > > You can do anything you like, but you'd better have good justification for > it. > Making ad hoc changes to force fields that were not necessarily designed to > do > what you think it should is generally very unwise. Whatever you do, make > changes in a local copy of the force field so you don't screw up other > simulations later on, or even better, make a special [atomtypes] directive > in > your .top file. > >> How I could prevent rotation of the lattice as the whole object ? ( >> simulation in vacuum in NVT) without any posres ? > > I can't think of a way to do this, nor would it have any real functional > purpose. You can remove rotation and translation afterwards with trjconv. > >> Its not possible to use very small box dimensions due to the rvdv= 1.4 >> in gromos ff >> (if I define box vectors compatible with the size of the lattice I've >> obtain error in grompp) > > If you're running in vacuo, you should turn off PBC and use infinite > cutoffs, > otherwise you likely will have periodicity artifacts and you are not truly > simulating in vacuo. > >> >> Also in connection to the above question with the box size I also >> wounder like to know how I could use ; periodic_molecules options >> with such lattice which asymmetric on left and right boundaries ( >> picture http://imageshack.us/photo/my-images/543/lattice.png/ ) ? >> > > Some boxes have hexagonal cross-sections (see the manual) that might be > useful. > In a basic sense, all you need to have is atoms that should be bonded to > one > another through a periodic boundary should be separated by one bond length > (i.e. > half a bond length on either side of the box) and make sure these bonds are > > added to the topology (probably by hand). Then the periodic_molecules > option > works its magic and you have an infinite lattice. > > -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