Justin,
thanks again for explanation. I've tried examine that parameters more carefully. E.g in my system with 2 atom types I defined in topology [ atomtypes ] ;name at.num mass charge ptype c6 c12 CH2 6 0.000 0.000 A 0.0023406244 4.937284e-06 ; CB CH1 6 0.000 0.000 A 0.0023406244 4.937284e-06 ; CA where both C6 and c12 values were coppied from simple C (carbon atom) ; C 6 0.000 0.000 A 0.0023406244 4.937284e-06 As I understood c6 correspond to the Rmin (sigma) term in LJ equation andc 12 is the pre-exponential (eps) factor which correspond to the potential dept. So why addition [ nonbond_params ] are needed where such interactions are presence for pair of that atoms ? ; i j func c6 c12 ; CH3 CH2 1 0.008473481 3.0084136e-05 In particular I'd like to change vdw radius for the selected atoms of my lattice ( by adding a new type for such atoms). 2) Could you also provide me some examples of the editconf parameters for box vectors and angles for definition of the new box types ? In particular I'd like to build pyramide-like box with the truncated top (like in the Maya's ancient temples) for my lattice. I've not found any reasonable tutorial for that. James 2013/1/3, Justin Lemkul <jalem...@vt.edu>: > > > On 1/3/13 2:01 PM, James Starlight wrote: >> 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 ? >> > > Not from the .rtp file, but the .top is overriding the contents of > ffnonbonded.itp. > > -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
