[gmx-users] Some Questions

[Omid Yazdan]

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?

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?

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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