Dear all,
I'm simulating P450 proteins currently and having issues with my simulation data not agreeing with experimentally obtained data. A helix, located immediately above the heme on the distal side, is either unravelling or distorting significantly during production MD runs, whereas crystal structures of identical/similar mutants indicate no such distortion from the WT. Briefly, I'm using GROMACS 2018.1 and the AMBER99SB-ILDN force field. I'm doing a 2 stage EM: Steepest Descent with a criterion of 500 kJ / mol nm followed by conjugate gradient (100 kJ / mol nm) and then position restrained NVT equilibriation with the v-rescale thermostat (200ps) followed by position restrained NPT with Berendsen barostat (I'm then changing to Parrinello-Rahman for the production runs.) I've tried altering time constants to no avail and was wondering if anyone had any ideas what might be causing this / places to focus my attention? I've included my .mdp parameters below for the production run. Many thanks, Matthew Fisher ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000000 ; 2 * 50000000 fs = 100000 ps (100 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 10.0 ps nstvout = 5000 ; save velocities every 10.0 ps nstfout = 5000 ; save forces every 10.0 ps nstenergy = 5000 ; save energies every 10.0 ps nstlog = 5000 ; update log file every 10.0 ps nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps compressed-x-grps = System ; save the whole system ; Bond parameters continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds are constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ; Buffered neighbor searching ns_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 298 298 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 5.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off -- 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 [email protected].
