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>
>
-- 
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

Reply via email to