[gmx-users] Re: Multiple protein simulations in a box
rajeswari.biotech at gmail.com
Mon Nov 5 06:04:17 CET 2012
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
>> 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.
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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