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

[Mark Abraham]

Hi,


On Mon, Nov 28, 2016 at 9:44 AM Mijiddorj Batsaikhan <b.mijiddorj at gmail.com>
wrote:

> 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?
>

Yes, for the non-stochastic integrators, it only affects the stochastic
temperature-coupling behaviour.


> (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
>

That's workable, but a zero tau_t means there is no weak relaxation
behaviour. Whether this is more or less unstable than a regime where there
is relaxation, e.g. tau-t=0.1 probably depends on how implausible the
starting configuration is. Equilibrating a membrane system takes at least
hundreds of nanoseconds, so most of your time will not be in a region where
there's lots of heat transferred (which is when it is useful to have no
weak relaxation behaviour).


> *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
>

Fine

Mark


> Best regards,
>
> Mijiddorj
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