Could you tell me what is the procedure to cut the bond to produce the photodissociation?
On Thu, Sep 20, 2012 at 3:12 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 20/09/2012 1:08 PM, Rajiv Gandhi wrote: > >> Dear all, >> >> Why all people cut the protein ligand bond to produce the >> photodissociation? >> > > Because MM forcefields typically assume bonds do not break or form. > Electronic degrees of freedom are not directly considered in the model. > > > For instances, In myoglobin, To simulate photodissociation of the CO >> complex, the Fe–CO bond of the >> starting structure was cut before any calculation.Fe-C bond were cut and >> instantaneously switch the heme force >> field from 6-coordinated Fe to that of the 5-coordinated Fe. >> >> >> >> I want to understand how we can delete this bond between Fe-CO to induce >> the photodisssociation ? After we cut the bond what it can do during MD >> simulation ? >> > > If you know enough about such a system to parametrize the bonded and > non-bonded systems, then in principle you could watch the process of > dissociation after cleavage. But I can imagine spending 6 months to do that > parameterization and still failing. A modelling approach that works nicely > for simple first- and second-row elements not undergoing chemical reactions > need not be extensible to either transition elements or reactions. > > Mark > -- > 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
