[gmx-users] umbrella sampling

[Justin A. Lemkul]

Poojari, Chetan wrote:
> Hi,
> 
> I am working on membrane protein.
> 
> In umbrella sampling tutorial.......we saw the pulling of the peptide A away from peptide B.
> 
> I want to pull the peptide deep into the hydrophobic core of the bilayer from outside (solvent environment).
> 
> Please can someone suggest me how to go about this.
> 

The same principles as in the tutorial apply.  Choose a reference group 
(membrane), a pull group (peptide), and a pull direction.  You'll have to 
empirically adjust pull rate, force constant, etc to properly treat your system.

-Justin

> 
> 
> Kind regards,
> chetan.
> 
> 
> 
> 
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-- 
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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

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