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

[Sidong Tu]

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?

Here is my full .mdp file:






































































*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