[gmx-users] Re: SMD - reproducibility

Steven Neumann s.neumann08 at gmail.com
Fri Apr 26 14:01:20 CEST 2013

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

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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