[gmx-users] Re: SMD - reproducibility

[rajendra kumar]

I am not sure but different force profiles may be due to the
non-equilibrium relaxation problem. The path on the energy landscape during
the non-equilibrium simulations depends on the pulling rate and/or
relaxation of any unknown coordinates correlated with pulling coordinates.
If during pulling, correlated coordinates will not be able to relax
completely, high energy path is more likely on the energy landscape. Effect
of relaxations can be tested by performing simulations at several reduced
pulling rate. Also, there are several literature available on the effect of
pulling rate during simulations.

With best regards,
Rajendra

On Fri, Apr 26, 2013 at 5:31 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> Thanks for this. I think option 2 is more reasonable. However, still do not
> know why I get sometimes 3 types of profiels and sometimes 10 for 10 SMD
> simulations...
>
> On Fri, Apr 26, 2013 at 12:46 PM, Thomas Schlesier <schlesi at uni-mainz.de
> >wrote:
>
> > Think i now understand your question. Forget what i wrote before.
> > I could imagine the the 'grompp -t npt.cpt' part is a problem.
> > If the simulations would be numerical reproducible, one should get the
> > same results. As they are not, the results will differ somewhat (would
> > think the more, the longer you simulate). But two different simulations
> > would be more equal to each other, than two simulations which start with
> > different velocity distributions for the particles.
> >
> >
> > If you're interested in an stochastic analysis of your system (meaning
> > simulations which are not equal - performing many pulling experiments in
> > reality, one would also have many different starting points) you could do
> > two things:
> > 1) Run a look npt simulation, and use different frames to start the SMD
> > simulations. From each frame the particles should have a different
> velocity
> > distribution and the results of the SMD simulations should also differ.
> > (Depending on how many SMD simulations you want to perform, this might
> get
> > expensive, since the starting frame for SMD should be separated by more
> > then a few ps.)
> > 2) Dump the 'npt.cpt' file and randomly determine new velocities for each
> > particle at the start of each SMD simulation. Since each simulation has a
> > different velocity distribution, the SMD simulation wont be the same.
> This
> > approach has only one weak point. Due to assigning new random velocities
> > you destroy the thermal equilibrium of the system. But if the system was
> > well equilibrated before, this distrubance should only be small and after
> > the first 100-200 ps of the SMD simulaton the system is in thermal
> > equilibrium. If the complete SMD simulation is much longer (couple of
> ns),
> > the interesting stuff would happen longer after the inital simulation
> time
> > with the destroyed equilibrium.
> >
> > Hope this helps
> > Thomas
> >
> >
> >
> > 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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