[gmx-users] Re: how is the pulling force measured

[alex.bjorling]

2013/4/30 kim2811 [via GROMACS] <ml-node+s5086n5007778h86 at n6.nabble.com>

>
> Hi Alex,
>
> I read the manual but I got confused with the details. My pull_geometry =
> position with pulling direction along y. I am trying to dissociate two
> interacting proteins. So I set the last amino acid of one protein as my
> reference group and the last amino acid of the other protein as the pulled
> group. Now, I don't know exactly how to interpret what reference group and
> pulled group mean, and what is their difference; since in the manual it
> says 'there is no difference in treatment of the reference and pulled group
> (except with the cylinder geometry).' Also, it says that measured force
> output is the force of the pulled group.
>

Ah. I think it would be wiser to use pull_geometry=distance, so that the
two groups (0 and 1, reference and pulled) are connected by a spring. It
might also be better to use groups bigger than one amino acid, but I guess
that depends on what you want to accomplish.

A very useful tutorial in which two interacting peptides are separated can
be found here:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html


>
> So basically, I am trying to visualize how the system works. Using the
> pull_geometry stated above, are the two groups (reference and pulled)
> attached to two virtual springs? Will this statement be correct?
>

I'm no expert and will have to leave this question unanswered. Sorry.


>
> "Force was applied by moving the clamped ends of the two springs (i = 1,
> 2) in opposite directions with constant velocity v to positions Zi(t) =
> zi(0) + vt, where zi(0) is the initial position of the end of the molecule.
> The forces fi(t) at the two ends were measured at every time step using the
> relationship fi(t) = k (zi(t) - Zi(t))."
>
> I hope my questions make sense. Thank you.
>
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