On 2012-10-15 05:54:58AM -0400, Justin Lemkul wrote: > > > On 10/15/12 5:45 AM, cuong nguyen wrote: > > Dear, > > > > The top file downloaded from PRODRG did not consist of [atomtypes]. Please > > tell me how can I add and use this function? > > > > I see no need to change anything about the L-J parameters. Is there some > reason > you believe them to be incorrect? If you modify L-J parameters, you're no > longer using Gromos96 43a1. In PRODRG topologies, the charges and charge > groups > certainly need changing, but I have never seen a need to hack the L-J > parameters. > > -Justin
I think he needs to go back and ask the authors of the paper he is trying to reproduce about how to parameterize 1-octanol according their specifications. If they are using different LJ for the atoms in this molecule from 43a1 then they are obviously not using gromos96 43a1 :) > > > Best regards, > > > > Cuong > > > > On 15 October 2012 16:43, Peter C. Lai <p...@uab.edu> wrote: > > > >> Is there no [atomtypes] section in the top file? > >> > >> On 2012-10-15 03:53:54PM +0800, cuong nguyen wrote: > >>> Thanks for you email. > >>> I already had the .gro and .top files from PRODRG. Now I want to > >> reproduce > >>> these files following the LJ parameters in a published paper (charge, > >> sigma > >>> and epsilon values). I can change the charge in the top file, yet I do > >> not > >>> know how to change sigma and epsilon values. > >>> > >>> Best regards, > >>> > >>> Cuong > >>> > >>> On 15 October 2012 13:57, Peter C. Lai <p...@uab.edu> wrote: > >>> > >>>> It's hard to understand your question. What do you mean by "reference > >>>> parameters"? You said you already obtained a .gro and .top from PRODRG, > >>>> which > >>>> uses the gromos 43a1 forcefield to derive the parameters, so if you > >> need > >>>> to change the LJ parameters, edit the top file it gave you. > >>>> > >>>> If you want to reproduce the results of a published paper, you should > >> use > >>>> the > >>>> forcefield and parameters specified in that paper and contact the > >> author(s) > >>>> if more details are needed. > >>>> > >>>> On 2012-10-15 10:42:57AM +0800, cuong nguyen wrote: > >>>>> Thank you very much for your email, Justin. > >>>>> in case I want to use the reference parameters, which force-field and > >>>> what > >>>>> should I do to get the .gro and .top files for this molecule? > >>>>> > >>>>> Best regards, > >>>>> > >>>>> Cuong > >>>>> > >>>>> > >>>>> On 12 October 2012 21:14, Justin Lemkul <jalem...@vt.edu> wrote: > >>>>> > >>>>>> > >>>>>> > >>>>>> On 10/12/12 8:04 AM, cuong nguyen wrote: > >>>>>> > >>>>>>> Dear Gromacs Users, > >>>>>>> > >>>>>>> I got the .gro and .top files of 1-octanol downloaded from PRODRG > >>>> website. > >>>>>>> Please let me know if I can change charge, epsilon and sigma of > >> the > >>>>>>> molecule as written in a paper? and How to do? > >>>>>>> > >>>>>>> > >>>>>> Atom types from PRODRG rarely, if ever, need changing. Charges > >> can be > >>>>>> taken first by chemical homology (group-based approach that makes > >>>> Gromos > >>>>>> force fields convenient) and then by calculating the charges > >> yourself. > >>>> For > >>>>>> 1-octanol, it should be very straightforward to obtain parameters, > >> zero > >>>>>> charges on all the C atoms except for the one in the alocohol, then > >>>>>> standard alcohol charges for the C-O-H. Whether or not those > >>>> parameters > >>>>>> are sufficiently accurate is up to you to decide, but that's the > >>>> approach > >>>>>> one would take with this particular force field. > >>>>>> > >>>>>> -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< > >>>> 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< > >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users> > >>>>>> * Please search the archive at http://www.gromacs.org/** > >>>>>> Support/Mailing_Lists/Search< > >>>> 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< > >>>> 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 > >>>> > >>>> -- > >>>> ================================================================== > >>>> Peter C. Lai | University of Alabama-Birmingham > >>>> Programmer/Analyst | KAUL 752A > >>>> Genetics, Div. of Research | 705 South 20th Street > >>>> p...@uab.edu | Birmingham AL 35294-4461 > >>>> (205) 690-0808 | > >>>> ================================================================== > >>>> > >>>> -- > >>>> 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 > >> > >> -- > >> ================================================================== > >> Peter C. Lai | University of Alabama-Birmingham > >> Programmer/Analyst | KAUL 752A > >> Genetics, Div. of Research | 705 South 20th Street > >> p...@uab.edu | Birmingham AL 35294-4461 > >> (205) 690-0808 | > >> ================================================================== > >> > >> -- > >> 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) 231-9080 > 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 -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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
