Hi, could you try to use the Morse potential for this bond. As far as I know, the parameters can be directly obatined forml the armonic potential expression.
Francesco 2012/9/21 Mark Abraham <mark.abra...@anu.edu.au> > On 21/09/2012 11:35 AM, Rajiv Gandhi wrote: > >> Dear all gromacs users, >> >> In myoglobin system, how we can cut the bond between Fe-C to produce the >> photodissociation through MD?. >> > > By not making it in your topology. Whatever procedure you follow for > making the other Fe-C interactions needs to differ from the one you wish to > model the cleaved bond. > > Mark > > > I have seen there are number of studies over photodissociation and also >> I believe that people have used their appropriate parameterization files >> to >> cut these bond. >> >> I am struct with this parameter and cutting bond process. It would be >> really appreciated if anyone can give some suggestion/information about >> this. Thanks a lot. >> >> >> Sincerely >> >> Rajiv >> > > -- > 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> > -- Cordiali saluti, Dr.Oteri Francesco -- 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
