[gmx-users] Re: SMD - reproducibility

Thomas Schlesier schlesi at uni-mainz.de
Fri Apr 26 13:46:56 CEST 2013

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

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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