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

[Justin Lemkul]

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

==================================================