[gmx-users] gen_temp, gen_seed

[Steven Neumann]

Dear Gmx Users, Dear Justin

I am wondering which approach for generating velocities in protein or
protein-ligand system is a proper one:

a)
NVT   gen_vel = yes
          gen_temp=298
          gen_seed=-1
NPT   gen_vel=no
MD    gen_vel=no

b)
 NVT   gen_vel = yes
          gen_temp=298
          gen_seed=-1
NPT   gen_vel=no
MD    gen_vel = yes
          gen_temp=298
          gen_seed=-1

As I always used the approach a) I saw in Justin's tutorial (Protein and
ligand) b). However, in protein in water tutorial he used the approach a).
I am confused, can you please help?

Thank you.

Steven
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