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

[Peter C. Lai]

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.

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