[gmx-users] Some Questions

David van der Spoel spoel at xray.bmc.uu.se
Sun Jul 15 18:28:06 CEST 2007

Omid Yazdan wrote:
> Dear Gromacs Users,
> I am relatively new to molecular dynamics field and I have some 
> questions in mind. Don`t worry! I wont ask silly questions!(or at least 
> I try to). I just want to direct my efforts in right way. My questions are:
> 1) Say we want to simulate a four-helix protein and we want to know how 
> strong these helices are packed together. So how can we calculate the 
> force (or work) needed, for example, to pull a helix apart from three 
> others? One solution may be to simulate the helices two times, one when 
> they are packed, and then when one helix is set apart, and then 
> calculate the energy difference. But you know better than me this is a 
> wrong solution. Another solution may be to use some "slow growth" 
> method. Any other suggestion?
check PNAS 104 (2007), p. 6206–6210
> 2) Another example. I want to put an increasing force at a N-terminal of 
> a helix and watch what happens to the helix as the force increases 
> during trajectory and find when the arrangement changes. Can I do that?
yes. use pull code.
> There may be direct and indirect ways to perform such tasks. Please tell 
> me if you aware of them. Any previous experience, especially published 
> articles, will be helpful.
> Thanks in advance
> Omid
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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