[gmx-users] Re: NPT simulation for mutation study (Justin A. Lemkul)

[Shyno Mathew]

Hey Justin,

thanks for your reply.
For gen_vel, the manual says "Generate velocities in grompp according to a
Maxwell distribution at temperature gen_temp [K], with random seed
gen_seed. This is only meaningful with integrator
md"
Since the integrator I am using is sd, I put 'gen_vel no'
Yes you are correct, this is equilibration.
>From what you are saying, even with sd as the integrator, I guess, I should
put
gen_vel       yes
gen_temp   310  ; i want to do the simulation at 310K

thanks

-- 
Shyno Mathew
PhD student
Department of Chemical Engineering
Columbia University
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