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

Justin Lemkul jalemkul at vt.edu
Sat Nov 3 14:55:43 CET 2012

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 




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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