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 [email protected]:
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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