there should be an extra option in your mdrun command line if reproducibility is an issue:
-[no]reprod bool no Try to avoid optimizations that affect binary reproducibility the value of -reprod is set to no by default, turn on that option and trajectories should be the same. best Andre On Fri, Apr 26, 2013 at 9:25 AM, Steven Neumann <[email protected]>wrote: > 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 <[email protected] > >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 [email protected]: > > > > 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<[email protected] > ** > >> >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< > [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 > >>>> >> > >>>> > >>> > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/**mailman/listinfo/gmx-users< > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > * Please search the archive at http://www.gromacs.org/** > > Support/Mailing_Lists/Search< > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting! > > * Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to [email protected]. > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > http://www.gromacs.org/Support/Mailing_Lists> > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- _____________ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? 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