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, 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 >> > > -- > 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
