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.
In
http://pubs.acs.org/doi/full/10.1021/jp3115644
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.
Greetings
Thomas
Am 26.04.2013 12:00, schrieb gmx-users-requ...@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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