[gmx-users] what's the difference between gen_seed and ld_seed?

Thomas Schlesier schlesi at uni-mainz.de
Fri Aug 24 12:00:03 CEST 2012

Am 23.08.2012 23:11, schrieb gmx-users-request at 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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