[gmx-users] replicates with different random seed
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>
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
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users