Am 23.08.2012 23:11, schrieb gmx-users-requ...@gromacs.org:
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.
Also the 'v-rescale' thermostat uses the ld_seed.
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