[gmx-users] protein crystallization

Justin A. Lemkul jalemkul at vt.edu
Mon Feb 2 16:37:35 CET 2009

Santan William wrote:
> Hello, users. Can Gromacs do protein crystallization simulations? I 
> tried looking for some information about it on mailings but failed. 
> Would anyone give me some advice how to do it? Thanks.

Well, Gromacs can technically simulate galaxies, so I guess anything is 
possible.  What you need to consider is whether or not such a simulation would 
be feasible.  Do you have parameters for any special solvents involved?  If not, 
the long road of parameterization lies ahead.  Is the system size feasible?  How 
many protein molecules will you be simulating?  And then the big one - is the 
timeframe feasible?  With Gromacs 4.0, simulations are running a lot faster than 
before (thanks developers!), but if you've ever done wet lab crystallization, 
you know that crystals develop only very slowly, over days or weeks even. 
Perhaps you can see the initial nucleation events in a simulation, but you may 
still be surpassing the microsecond time scale to do so, again depending on the 
size of your system.


> Best,
> william
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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