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?
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?
thank you very much
best
Albert
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