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

[Justin Lemkul]

On 8/23/12 2:06 PM, 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.
>
> I am just wondering which option would be better for our simulations?
>

Regenerating velocities at each step negates the purpose of previous 
equilibration.  You should generate velocities only once.  Note that gen_seed is 
ignored if gen_vel = no.

> 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?
>

Which integrator are you using?  For the md integrator, ld_seed is irrelevant. 
For sd and bd, it is pertinent.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================