[gmx-users] Pulling Simulation Query

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 27 13:58:19 CEST 2010

Natalie Stephenson wrote:
>  Hi ...
> Just wondering if there's a way, during pulling simulations, to 
> immobilise say the C-terminus of the protein. 
> I've been running through the 'Umbrella Sampling' tutorial with my own 
> protein.  Within this tutorial the ChainB is used as the immobile 
> reference - so it is this that is position restrained.  Is there a way 
> of position restraining just one amino acid? How would I specify that in 
> the topology file?

Use genrestr with a custom index group to generate a posre.itp file for that 
residue.  Then, #include this new .itp file in your .top (just like what the 
tutorial does).


> Thanks
> Natalie


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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