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? 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