Hi users, I did energy minimization of a protein complex using the following minimization mdp file.
; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1.0 kJ/mol emstep = 0.01 nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 10 ; Write energies to disk every nstenergy steps energygrps = Protein ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.4 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) and the pr.mdp = ; VARIOUS PREPROCESSING OPTIONS title = Position Restrained Molecular Dynamics define = -DPOSRES constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 25000 ; total 50 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout = 500 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 and md.mdp file = ; VARIOUS PREPROCESSING OPTIONS title = Position Restrained Molecular Dynamics ; RUN CONTROL PARAMETERS constraints = all-bonds integrator = md dt = 0.002 ; 2fs ! nsteps = 2500000 ; total 5000 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout = 0 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 The minimization step went well. but while doing the final mdrun am getting LINCS error. i read through the numerous mailing list on grimaces but still couldn't understand how would i fix this. am getting this error for all the 10 protein complex i did minimization for. Please help. Thanks, Aiswarya
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