[gmx-users] on the Umbrella Sampling tutorial

[Justin A. Lemkul]

Acoot Brett wrote:
> Dear All,
>  
> According to the on-line tutorial on Umbrella Sampling, there is a step 
> to get a lot of configurations, and for each configuration we need to 
> run a MD. For this reaon I regard the Umbrella Sampling method for 
> binding energy calculation is not suitable for relatively large protein 
> complex (I am not sure the MW of the complex used by Justin in the 
> original publication. But for my protein-ligand complex, the total MW is 
> about 50, 000 Dalton), as for the MD for all the configurations will 
> take a rather long calculation time.
>  
> Do you agree on my view? Or do you have much better method?
>  

Umbrella sampling is inherently very demanding in terms of the time and 
resources necessary.  For determining accurate binding energies for protein 
complexes, I don't think there is a fast way using any technique.

-Justin

> Cheers,
>  
> Acoot
> 
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Acoot Brett <acootbrett at yahoo.com>; Discussion list for GROMACS 
> users <gmx-users at gromacs.org>
> *Sent:* Tuesday, 3 April 2012 8:59 PM
> *Subject:* Re: [gmx-users] on the Umbrella Sampling tutorial
> 
> 
> 
> Acoot Brett wrote:
>  >
>  > Dear All,
>  >
>  > For the on-line Umbrella Sampling tutorial 
> "http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/04_EM_equil.html" 
> of *Justin Lemkul*, will you pleasse tell me for the equilibration where 
> there is no NVT equilibration?
>  >
> 
> It wasn't necessary.  The system is quite robust and my experience has 
> indicated that NPT equilibration was sufficient.
> 
> -Justin
> 
> -- ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================