[gmx-users] Re: gmx-users Digest, Vol 108, Issue 165

Thomas Schlesier schlesi at uni-mainz.de
Fri Apr 26 12:42:36 CEST 2013

TL;DR version (longer version below):
Due to the stochastic nature of SMD (and pulling experiments in general) 
it is quite natural that the results for different simulations will not 
be excatly the same.

I would say you are fine. Thing is, if you do ligand unbinding SMD 
simulations the unbinding process is a stochastic process and the 
results differ somewhat, most importantly the rupture force (highest 
force before the rupture event) will differ between the simulations and 
you'll get a distributions of rupture forces.

In a simple two-state model, the slope of force vs time, should be the 
same for each simulation before and after the rupture event (but 
probably different slopes before and after the rupture), only the time 
when the rupture event happens will change.
If your system is more complex (say a couple of bonds must be broken 
before the ligand unbinds), the slope before the rupture may vary 
between some simulations (in some simulations some of the bonds break 
earlier than in other simulatons.

i looked into a system which can be described by a two-state model. The 
results from one typical trajectory are shown, but mostly i discuss the 
averaged results. If one compares the single trajectory and the 
averaged, one clearly sees that the trajectories varies around the 
rupture event, but at the start of the simulations the system behaves 
almost equal for each simulation.
Hope this helps.


Am 26.04.2013 12:00, schrieb gmx-users-request at gromacs.org:
> Dear Users,
> I am running my puling simulations of ligand with constant velocity. First
> I minimize and equilibrate my system:
> grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr
> mdrun -s em.tpr -deffnm em
> grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr
> mdrun -s nvt298.tpr -deffnm nvt298
> grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p
> topol.top -o npt298.tpr
> mdrun -s npt298.tpr -deffnm npt298
> Then I run 10 pulling simulations with the same mdp file:
> grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o
> pull_1.tpr
> mpiexec mdrun -s pull_1.tpr -deffnm pull_1
> ...
> grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o
> pull_10.tpr
> mpiexec mdrun -s pull_10.tpr -deffnm pull_10
> I get 3 different (but similar) profiles (Force vs time) with 10
> simulations as some of them produce exactly the same results... In another
> system with the same methodology I get 10 similar but different profiles. I
> am wondering why in this case only 3 types are possible... Shall I try
> grompp without -t npt.cpt ?
> Steven

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