Varsha: have you subscribed to the list yet? Please do so if you haven't. On Sun, 2009-03-22 at 13:18 +0400, varsha gautham wrote: > 3. hen how to choose a timestep for a simulation like a picosecond or > a nanosecond?What is a timestep? > > I have gone through many materials and stuffs related to Gromacs.But i > dint get a clear idea, addressing this 2 questions.I will be really > thankful if someone took time to read to this mail patiently and reply > me with a solution which am looking for months together.Thanks in > advance.
The time step is the step used in integrating the equations of motion (F = ma). The algorithm used to integrate the equations is leap-frog, which you can look up in the manual (eqns 3.20 and 3.21). The timestep in GROMACS is usually of the order of femtoseconds (1 fs = 0.001 GROMACS internal units). To determine what time step to use for your system turn off all pressure and temperature couplings (NVE ensemble) and run a few short simulations with different time steps. Look at the potential, kinetic and total energy output of the runs: if the total energy stays constant the time step is sufficiently small. -- ------------------------------------------------------ Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 ------------------------------------------------------ Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi ------------------------------------------------------ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
