[gmx-users] Are the v-rescale thermostat and ld-seed suitable with md integrator?

[Mijiddorj Batsaikhan]

Dear gmx_users,

Hello, my simulation system consists of a protein and membranes using
GROMACS. Initial structure was generated by Charmm-gui that gave the
appropriate mdp files for the simulation. During the equilibration stage,
Berendsen thermostat does not generate the correct kinetic energy
distribution, and V-rescale thermostat is recommended by grompp.

>From the manual, v-rescale needs to set the random seed with *ld-seed*.
This thermostat works correctly even for *tau-t = 0*.

I have two questions.

(1)

I want to use md integrator, Is *ld-seed* agreeable with md integrator?

(2)

I used following options for NVT and NPT equilibration.

Are the options correct?

*For NVT:*
tcoupl = v-rescale
tc_grps = PROT MEMB SOL_ION
tau_t = 0 0 0
ref_t = 298 298 298
ld-seed = -1


*For NPT:*

tcoupl = v-rescale
tc_grps = PROT MEMB SOL_ION
tau_t = 1.0 1.0 1.0
ref_t = 298 298 298
ld-seed = -1

Best regards,

Mijiddorj