[gmx-users] Re: SMD - reproducibility

[Steven Neumann]

Thanks anyway. I will try tu pull it 20-40 times to tell something.

Steven

On Fri, Apr 26, 2013 at 1:23 PM, Thomas Schlesier <schlesi at uni-mainz.de>wrote:

> 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 direction.
> 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@**gromacs.org<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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