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

[Justin Lemkul]

On 11/28/16 3:44 AM, Mijiddorj Batsaikhan 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?
>

Why wouldn't it be?  It's only used for the random seed for the v-rescale 
thermostat in this context.

> (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
>

Both are just thermostat options, they don't distinguish between NVT and NPT. 
For NPT, you need a barostat as well.  I have never run with tau-t = 0 even 
though the manual says it works.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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