Thanks Ross. I'll definitely go through the suggested paper and books.
Soumya
On Mon, Aug 20, 2012 at 11:36 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Dear Soumya,
>
> There is no such thing as the 'correct' structure. I suggest reading a
> textbook on basic statistical mechanics so you understand the concept of
> phase space and partition functions. You might also want to take a look at
> the following publication:
>
> Pierce, L.C.T.,; Salomon-Ferrer, R.; de Oliveira, C.A.F.; McCammon, J.A.;
> Walker, R.C., "Routine access to millisecond timescale events with
> accelerated molecular dynamics.", Journal of Chemical Theory and
> Computation, 2012, in press, DOI: 10.1021/ct300284c
> <http://dx.doi.org/10.1021/ct300284c>
>
>
> This should give you an idea of the sorts of things you can use
> accelerated MD for. In particular note the discussion on the number of
> different long lived states that are sampled. Also take a look at the
> supplemental material which provides details of what we believe is a
> robust method for selecting appropriate boost parameters.
>
> In short aMD is a very advanced method and you should make sure you
> understand the basics of molecular dynamics and statistical mechanics and
> appreciate the theory behind the method before using it.
>
> All the best
> Ross
>
>
>
> On 8/19/12 10:15 PM, "Soumya Lipsa Rath" <soumyalipsabt.gmail.com> wrote:
>
> >Dear Amber Users,
> >
> >I have run accelerated MD using Amber12 using default value of 0.2 for
> >calculating alphaD, alphaP, EthreshD and EthreshP as specified in the
> >manual.
> >I also tried few test runs by using values 0.5 and 1 instead of 0.2 to see
> >its effect of the MD. All of them result in different structures after
> >simulation. How do I know which one of them is the correct run?
> >
> >Thanks,
> >
> >Soumya
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>
>
>
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Received on Mon Aug 20 2012 - 00:30:04 PDT
