Hi,
kinetic constants calculations are very demanding and non trivial at
all. There are several methods, but in my opinion few are very reliable.
First of all you can search for the Markov state approach (i.e. have
look to this
http://scitation.aip.org/content/aip/journal/jcp/134/17/10.1063/1.3565032 <
https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fscitation.aip.org%2Fcontent%2Faip%2Fjournal%2Fjcp%2F134%2F17%2F10.1063%2F1.3565032>
and related ref of Noe' F.). Another approach is based on joining
metadynamics and Markov theory
(
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000452
<
https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fjournals.plos.org%2Fploscompbiol%2Farticle%3Fid%3D10.1371%2Fjournal.pcbi.1000452>
and
http://pubs.acs.org/doi/abs/10.1021/ja903045y
<
https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fpubs.acs.org%2Fdoi%2Fabs%2F10.1021%2Fja903045y>).
Finally you can read this last very interesting approach using smoothed
potential
http://www.nature.com/articles/srep11539?message-global=remove
<
https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fwww.nature.com%2Farticles%2Fsrep11539%3Fmessage-global%3Dremove>.
HTH
and
On 02/12/2015 14:34, Jason Swails wrote:
>
> On Wed, Dec 2, 2015 at 7:14 AM, Ziba Bahadori <ziba_bahadori.yahoo.com>
> wrote:
>
>>
>> Hi every oneI have a questionCan I use amber for kinetics studies?how?
>>
> This question is so vague as to have no good answer. There are many
> kinetic studies you can do with packages like Amber, and many that you
> cannot. Since the answer for the first question is both "yes" and "no",
> the answer for the second is undefined. It depends on many factors (what
> you're trying to learn, what approximations you are prepared to deal with,
> the computational resources you can devote to it, what you *know* about the
> process, etc.). Kinetics is a very broad area -- you have diffusive
> processes (where diffusion is rate-limiting), chemical reactions with bonds
> breaking/forming, binding events, folding/unfolding, ... etc.
>
> This question suggests that your next step should be a literature review,
> paying particular attention to articles that study similar things to what
> you are trying to do.
>
> HTH,
> Jason
>
--
Andrea Spitaleri PhD
Istituto Computational mOdelling of NanosCalE and bioPhysical sysTems -
CONCEPT LabItaliano di Tecnologia
Via Morego, 30 16163 Genova
cell: +39 3485188790
http://www.iit.it/en/d3-people/andrea-spitaleri.html
ORCID: http://orcid.org/0000-0003-3012-3557
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Received on Fri Dec 04 2015 - 06:30:05 PST
