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: *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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
