[gmx-users] Fwd: tau-t effects on sd integrator

[Sidong Tu]

Thank you very much, Justin. I'll go and try with 2ps.


Best wishes,
Sidong

On Mon, Aug 29, 2016 at 1:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/29/16 1:29 PM, Sidong Tu wrote:
>
>> Dear all,
>>
>> I was trying to simulate lysozyme and polymer in water model tip3p using
>> charmm36 force field at 500K on Gromacs 5.1.2. The software ran on GPU and
>> the system size was about 60,000 atoms. I used sd as integrator and the
>> tau-t option was 0.1. I wondered if there is any problem with this option
>> for the suggested tau-t is 0.2 in manual. If is, how this influence the
>> result?
>>
>>
> I don't know where you see a recommendation of 0.2 as tau-t.  See
> http://manual.gromacs.org/documentation/5.1.2/user-guide/
> mdp-options.html#run-control
>
> "When used as a thermostat, an appropriate value for tau-t is 2 ps, since
> this results in a friction that is lower than the internal friction of
> water, while it is high enough to remove excess heat NOTE: temperature
> deviations decay twice as fast as with a Berendsen thermostat with the same
> tau-t."
>
> With a very low tau-t and SD, you probably have strongly over-damped
> dynamics.
>
> -Justin
>
> Here is my full .mdp file:
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>> *title                    = protein in watercpp                      =
>> /lib/cpp;define                  = -DPOSRES; RUN
>> CONTROLintegrator               = sdnsteps                   =
>> 100000000dt                       = 0.002; NEIGHBOR
>> SEARCHINGnstlist                  = 50cutoff-scheme            =
>> verletns_type                  = gridpbc                      =
>> xyzrlist                    = 1.2; OUTPUT CONTROLnstxout
>> =
>> 0nstvout                  = 0nstxtcout                =
>> 5000nstlog                   = 5000constraints              =
>> h-bondsconstraint_algorithm     = LINCSlincs-iter               =
>> 1lincs-order              = 6nstenergy                =
>> 5000continuation             = yes; OPTION FOR ELECTROSTATIC AND
>> VDWcoulombtype              = PMErcoulomb_switch          =
>> 0rcoulomb                 = 1.2; Dielectric constant (DC) for cut-off or
>> DC
>> of reaction fieldepsilon_r                = 1; Method for doing Van der
>> Waalsvdw-type                 = Cut-offvdw-modifier                 =
>> force-switch; cut-off lengthsrvdw_switch              =
>> 1.00rvdw                     = 1.20; Apply long range dispersion
>> corrections for Energy and PressureDispCorr                 = No;
>> Extension
>> of the potential lookup tables beyond the cut-offtable-extension
>> =
>> 2.5; Spacing for the PME/PPPM FFT gridfourierspacing           = 0.12; FFT
>> grid size, when a value is 0 fourierspacing will be
>> usedfourier_nx               = 0fourier_ny               =
>> 0fourier_nz               = 0; EWALD/PME/PPPM
>> parameterspme_order                = 4ewald_rtol               =
>> 1e-05ewald_geometry           = 3depsilon_surface          =
>> 0optimize_fft             = no; OPTIONS FOR WEAK COUPLING
>> ALGORITHMStcoupl                   = v-rescaletc_grps                  =
>> Protein_NAG Water_and_ions Polymertau_t                    = 0.1 0.1
>> 0.1ref_t                    = 500 500  500Pcoupl                   =
>> Parrinello-Rahmanpcoupltype                       = isotropic; Time
>> constant (ps), compressibility (1/bar) and reference P
>> (bar)tau_p                    = 2.0compressibility          =
>> 4.5e-5ref_p                    = 1.0refcoord_scaling         =
>> comgen_vel                  = nogen_temp                 = 500; OPTIONS
>> FOR
>> LANGEVIN DYNAMICSld-seed                  = -1*
>> Best wishes,
>> Sidong
>>
>>
> --
> ==================================================
>
> 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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