[gmx-users] Re: SMD - reproducibility

Thomas Schlesier schlesi at uni-mainz.de
Fri Apr 26 14:23:24 CEST 2013

Don't know. One idea i have: Take a flexible and a relative rigid system 
and perform simulations with the same starting conditions (-> using -t 
*.cpt). I would imagine that for the flexible system the trajectories 
start earlier to deviate, since more stuff could happen (system is more 
flexible -> greater configurational space). For the rigid system the 
configurational space is smaller, so the probability is higher to always 
follow the same trajectory if one starts with a predefinded velocity and 
But don't know if this is true, but it's the first thing which comes to 
my mind.

Am 26.04.2013 14:01, schrieb gmx-users-request at gromacs.org:
> 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, schriebgmx-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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