Re: [AMBER] Accelerated Molecular Dynamics in Amber12

From: Ross Walker <>
Date: Sun, 19 Aug 2012 23:06:13 -0700

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

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

On 8/19/12 10:15 PM, "Soumya Lipsa Rath" <> 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
>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?
>AMBER mailing list

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Received on Sun Aug 19 2012 - 23:30:04 PDT
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