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-requ...@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<schl...@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-requ...@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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