[gmx-users] Steered MD in reverse direction?

[Justin A. Lemkul]

Sanku M wrote:
> Hi,
>   I am performing steered Molecular dynamics simulation to pull a 
> molecule out of a complex. I am using gromacs 4.5.4 to perform the 
> constant rate pulling..I have done the steered MD simulation in a 
> particular direction i.e hav pulled the molecule out of complex.
> But, to check the convergence/hysterisis of the pulled path way, I would 
> like to perform the same steered MD in reverse direction i.e push the 
> molecule back into the complex. But, I was wondering, to perform the 
> backward steered MD, how should I modify the .mdp parameters?  Should I 
> make the pull_rate1 negative or switch the pull_group0 and pull_group1 ? 
>  Any help will be appreciated.
> 

Use a negative pull rate.  But simple pulling like this can be difficult; you're 
now trying to hit a moving target.  A slight rotation of the protein can render 
the whole simulation junk - your pulled molecule may smack into some undesired 
location.

-Justin

> The following is the part of the pull-code parameter I am using:
> ; Pull code
> pull            = umbrella
> pull_geometry   = distance  ; simple distance increase
> pull_dim        = N N Y
> pull_start      = yes       ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = Mol_A
> pull_group1     = Mol_B
> pull_rate1      = 0.0025      ; 0.01 nm per ps = 10 nm per ns
> pull_k1         = 1000      ; kJ mol^-1 nm^-2
>   
> 
> Sanku
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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