On Wed, Mar 27, 2013 at 9:57 AM, 라지브간디 <ra...@kaist.ac.kr> wrote:
> Thanks for the mail justin. > > > In charmm27.ff, the value for bonded are in b0 and ko format, whereas the > gromos uses them in different way? If so, how do i convert between them? > > Please consult the manual, Chapters 4 and 5 for all the relevant equations and implementation. > > The value i incorporated for specific atoms are from published journals. > Thanks in advance. > > I think you're missing my point though. Just because something is published, doesn't mean you can use it for whatever purpose you like. People spend years working out properly balanced force fields, and if you try to put in some new atom type, it upsets the balance of every interaction. You may be OK within the context of CHARMM (depending on what the paper is, and what parameter set they modified), but I can guarantee you that if you're trying to incorporate CHARMM parameters into GROMOS, all you're doing is producing a pile of trash. You can probably "make it work" from a topology standpoint, but you shouldn't be doing it. I hope my perspective is clear; I'm trying to save you from wasted effort. -Justin > > > On 3/27/13 2:15 AM, ��������������� wrote: > > Hello gmx, > > > > > > I have LJ parameter value of C (epsilon = 0.0262 kcal/mol, sigma = 3.83) > O (epsilon = 0.1591. sigma = 3.12) in charmm format and wants to use them > in gromos43a1 or charmm27 force field in gromacs. > > > > > > Could you tell me how do i convert them to gromacs format? Any examples > plz. > > > > > > Equation 5.1 in the manual, or apply g_sigeps. Note that picking values of > atoms randomly and inserting them into an existing force field is a great > way to > completely invalidate the force field. Atom types are balanced against one > another. Making ad hoc changes means you're using an unvalidated parameter > set, > and any good reviewer is going to have serious issues with whatever data > you > produce. > > -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 > -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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
