Hi, many thanks for your answer. >> Any dynamical simulation has a lowest-energy structure... whether this means anything is another question.
I am just wondering whether the structures you find with MD determined mainly by thermodynamics (i.e. the lowest energy structures) or by kinetics (i.e. the structures with the lowest activation barriers)? I wonder to know how can I set the parameters and in which condition I obtain the structure by thermodynamics, and in which condition (with which parameter setting) I can obtain the structure by kinetics. >> MD samples the free-energy surface. Its shape and the temperature determine what structures might be found, and in what proportions. Do you mean that I can obtain the structure by thermodynamics in longer and higher temperature ; obtain the structure by kinetics in shorter and lower temperature? 2011/9/26 Mark Abraham <mark.abra...@anu.edu.au> > On 26/09/2011 6:41 AM, xiaojing gong wrote: > >> Dear all， >> A question about, in MD, in which situation you can obtain a structure >> with lowest energy. >> > > Any dynamical simulation has a lowest-energy structure... whether this > means anything is another question. > > > Can MD simulate the kinetics process, and obtain a stuctrue with the >> lowest activation barriers? >> > > Mapping free-energy surfaces where bonds are not made or broken can be done > with conventional MD. > > > Typically, are the structures we find with MD determined mainly by >> thermodynamics or by kinetics ? >> > > MD samples the free-energy surface. Its shape and the temperature determine > what structures might be found, and in what proportions. > > 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> >
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