Dear Thomas
One quick question first, is it unfolding the secondary structures or
separating the two components of the dimer?
Best wishes,
Romelia
> Dear Romelia and other AMBER users/developers,
>
> Thanks for the clarification. I have tried the rule of thump to select E
> and alpha values, which is described both in the recent paper you cited
> and
> the manual. Namely, to decide the dihedral boost parameters (Ed, aD) and
> the potential boost parameters (Ep, aP) I did:
>
> Ed=Ed_average+4*ResNum
> aD=4*ResNum*0.2
> Ep=Ep_average+0.16*AtomNum
> aP=0.16*AtomNum
>
> However, these parameter values lead to the unfolding of my protein dimer.
> I have also tried setting aD=4*ResNum*0.4 but I still observe the same
> effect.
> How would you recommend making the boost smoother? By increasing just the
> alpha values? Do I need to increase both of them?
>
> thanks in advance,
> Thomas
>
>
>
>
> On 27 September 2012 01:27, Romelia Salomon <romelia.caltech.edu> wrote:
>
>> Hi Thomas
>>
>> I added comments to your questions bellow.
>>
>> > Dear Amber users,
>> >
>> > I want to monitor the dynamics between a hetero-dimeric helical bundle
>> and
>> > a peptide. It is believed that the peptide binds at the
>> protein-protein
>> interface of the dimer and unwinds the helix of one of the components.
>> For
>> > this purpose I am considering accelerated MD (aMD) but have some
>> queries
>> about it:
>> >
>> > 1. Unlike Metadynamics, the bias in the potential is not history
>> dependent,
>> > therefore the system may explore multiple times the same area of
>> conformational space. Is this correct?
>>
>> This is correct, AMD will make it more probable to move out of deep
>> stable
>> basins in the conformational space and there is no mechanism to prevent
>> it
>> from going back.
>>
>> >
>> > 2. Is it possible to find the predominant conformations of the complex
>> from
>> > an aMD trajectory, namely the ones that we would expect to observe the
>> most
>> > in an unbiased MD trajectory?
>>
>> Yes, what you will get in the end of the AMD calculation is a state
>> distribution, that although is not the unbiased (canonical) one, it
>> still
>> holds some resemblance to it. AMD distributions can be re-weighted to
>> produce Boltzmann distributions.
>>
>> Please refer to these papers for more information.
>> (a recent paper we just published on the GPU implementation of AMD)
>> http://pubs.acs.org/doi/abs/10.1021/ct300284c
>> (one of the main papers for this method)
>> http://www.cse.nd.edu/~izaguirr/HaMM04.pdf
>>
>>
>> I hope this helps, let me know if you need more information.
>>
>> Best,
>>
>> Romelia
>
--
****************************************
Romelia Salomon
Walker Group
398 San Diego Supercomputing Center
UC San Diego
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 19 2012 - 09:00:04 PST
