[gmx-users] replicates with different random seed

Alex nedomacho at gmail.com
Tue May 8 11:13:40 CEST 2018

Ideally, you should repeat your entire procedure with a new seed from the
step that first generates velocities.

Repeating hundreds of nanoseconds of simulation a few times probably would
not be my response to your likely 85 year old reviewer, but I hope this


On May 8, 2018 2:58 AM, "vijayakumar gosu" <vijayakumargosu at gmail.com>

Hello all,

I have submitted a paper with 100ns simulations data, however reviewer
suggested to provide replicates with different random seeds. I have used
below lines in the mdp file of equilibration step for my first simulation.
now i am confused  for replicates (minimum 2) whether i have to start from
equilibration step or i can start from production step using the npt.gro
and npt.cpt from first simulation. additionally, I assume that when we have
( for example 3 replicates) we have to consider the average from the 3
simulations data. Please advise me whether my approach is reliable...


; Velocity generation
gen_vel = yes
gen_temp = 300
gen_seed = -1

Thanks in advance


Vijayakumar Gosu

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