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

[Mijiddorj Batsaikhan]

Dear Justin and Mark,

Thank you very much.


Best regards,

Mijiddorj


> Message: 1
> Date: Mon, 28 Nov 2016 08:37:02 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Are the v-rescale thermostat and ld-seed
>         suitable with md integrator?
> Message-ID: <78b04a1b-c26d-ffed-ea21-35238530ed4e at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> 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
>
> ==================================================
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 28 Nov 2016 13:40:01 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Are the v-rescale thermostat and ld-seed
>         suitable with md integrator?
> Message-ID:
>         <CAMNuMATB8_hvPU9R65tE3f-xGdmUAU2LV9ZsXtF=NAmrAc4Q7g@
> mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> 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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>
>