[gmx-users] Re: Final state not reached in pulling simulation

[Justin A. Lemkul]

On 7/13/12 2:32 AM, Neeru Sharma wrote:
> Dear Justin,
>
> Thanks for the suggestion regarding the pull force.
> 1)I will try by reducing the pull force to 1000 and 100 KJmol/nm2 now.
> Regarding the force being applied in z-direction, after visualizing my
> trajectory i thought it would work by providing force in z-direction.
> 2)Regarding the protein rotation, it does not rotate over the time. There
> are just some localized changes in it.
> 3)Regarding the distance measurement, I am measuring the distance between
> the specific atoms of the residue and the atoms of the GTP. Till now, these
> distances as well as the overall protein geometry is maintained well in the
> range too.
> 4)If this kind of pulling does not work out in my case, I will again try it
> with using "position" geometry too with pull_vec1.
>
> Can you suggest why have I not reached the final distance at the end of the
> simulation? Is it because of the geometry that I have used, because the
> force constant is already too high in this case?
>

I don't know why this is happening.  That's why you need to try more things to 
see if you can root out the issue.  There are a whole host of factors that can 
act against the pulling force.  You're not using any sort of position 
restraints, are you?

The other thing to keep in mind is that if your initial distance is 0.7 nm, and 
you pull for 10 ns at 0.05 nm/ns, you should in theory end up with a distance of 
0.2 nm, not 0.3 nm.  That is, assuming that the pulled group is free to move and 
thus smoothly goes along with the spring.  Other forces within the structure may 
act in opposition.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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