[gmx-users] Re: Multiple protein simulations in a box

[Rajeswari A.]

Thank you Justin for your suggestions and Rama for your reference..


On Sat, Nov 3, 2012 at 7:25 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/3/12 1:32 AM, Rajeswari A. wrote:
>
>> Thank you Rama and Justin for ur kind reply.
>>
>> @Justin: May i request you to kindly direct me to some references of
>> multiple protein simulation in a box using standard MD? And i have seen
>> the
>> tutorial about multi protein simuation is under development. May i know
>> when can we expect it to be ready? Once again i thank you for ur reply.
>>
>>
> Probably not any time soon.  It has been a low priority for me.  It won't
> be much of a tutorial, really, since the simulation itself is like any
> other protein-in-water system.  The only challenge is getting the proteins
> placed in a box with a sensible topology associated with the system.
>
>
>  @Rama : I want to study protein aggregation.
>>
>>
> There are numerous papers studying protein aggregation, including
> atomistic and coarse-grained models, using standard MD, REMD, and discrete
> MD.  Most of the ones I'm familiar with involve amyloidogenic peptides, but
> there may be others.  I'll shamelessly plug one of my own, but there are
> many, many more from other groups.
>
> http://pubs.acs.org/doi/abs/**10.1021/bi300113x<http://pubs.acs.org/doi/abs/10.1021/bi300113x>
>
>
> -Justin
>
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> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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