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
--
========================================
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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