Bogdan,
thanks againfor explanation. So if I have force field with the C6/C12 terms (instead of sigma\epsilon) I need to express sigma (which correspond to the Rmin in LJ equation) as the (C12/C6)^0.5. Than if I want to increase sigma ( and consequently to increase vdw radius of my atom) I must to increase c12 or decreace C6 terms. Does it correct in general ? 2013/1/17 Bogdan Costescu <bcoste...@gmail.com>: > On Thu, Jan 17, 2013 at 10:59 AM, James Starlight > <jmsstarli...@gmail.com> wrote: >> thank you for so detailed explanation. > > You're welcome. Now it's up to you to use it :) > >> Now it's only intresting to me >> if it possible to change vdw radius (assuming it as the distance from >> center of atom to it outer electronic shell)? > > Yes, it's possible. > >> E.g I want to change >> such value for each node in my lattice model (e.g for CH2 united atom >> that value might be > 1.5 and I want dicrease it to the 1 A ( as for >> simple carbon). Might I do it via some simplest modifications in the >> nonbonded.itp or should I do that by means of changes in >> sigma/epsillon terms (Which I also must express from A(c6) and B(c12) >> based on gromac's combination rules) ? > > If nonbonded.itp for your chosen force field is expressed in > sigma/epsilon (I guess that this is the case because you talk about an > existing value for sigma), then it's only a matter of changing the > sigma parameter of that atomic species. > > Keep in mind that this is only a description of the change - it > doesn't guarantee that the change is valid. If I'd be a reviewer I'd > ask for a reason for changing one of the parameters (sigma) and > keeping the other (epsilon) constant. > > Cheers, > Bogdan > -- > 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