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

[Albert]

hello guys

   I am producing MD production. That's really helpful.

thank you very much
best
Albert


On 08/23/2012 08:09 PM, Justin Lemkul wrote:
>
>
> 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
>