On 2012-08-23 08:06:12PM +0200, Albert wrote: > hello : > > I am a little bit confused about the difference between gen_seed and > ld_seed. I checked the manual, it is said: > > gen_seed > used to initialize random generator for random velocities, when gen_seed > is set to -1, the seed is calculated from the process ID number. > This is often used coupled with gen_vel which is Generate velocities in > grompp according to a Maxwell distribution at temperaturegen_temp [K], > with random seed gen_seed. This is only meaningful with integratormd. > > As indicated in Jonhn E.Kerrigan's tutorial, gen_seed=-1 is always > turned on in NVT, NPT and MD production step. However, in Justin's > Lysozyme in Water tutorial, this option is only turned on in NVT and the > following NPT and MD production were turned off.
Yes because you undo your equilibration when you reassign initial velocities using gen_seed in NPT and MD production (NPT) (md/md-vv integrator). > > I am just wondering which option would be better for our simulations? > > How about ld_seed? here is the statement from manual: > > ld_seed: (1993) [integer] > used to initialize random generator for thermal noise for stochastic and > Brownian dynamics. When ld_seed is set to -1, the seed is calculated > from the process ID. When running BD or SD on multiple processors, each > processor uses a seed equal to ld_seed plus the processor number. > > when should we turn this option on? As stated, you use this option for use with the bd or sd integrators. -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
