Dear Gromacs Users, I am using ver 4.5.1.
I completed a 500 ps run of NPT (the mdp file is below). after when i try to do a prod run with both velocity and pressure read from the output of NPT, I get a error newgrompp -f eq3npt.mdp -o eq3npttpr.tpr -p dimertop.top -c eq2nptpdb.pdb -t eq2npttrr.trr -e eq2nptedr.edr ********** READ 3 BOX VELOCITIES FROM eq2nptedr.edr ------------------------------------------------------- Program newgrompp, VERSION 4.5.1 Source code file: enxio.c, line: 1022 Fatal error: Could not find energy term named 'Xi-0-Protein' For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- I cannot judge where I go wrong. Kindly help. Best, nahren *********** **** mdp file ******* define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 250000 ; 2 * 250000 = 500 ps dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 0.2 ps nstvout = 500 ; save velocities every 0.2 ps nstenergy = 250 ; save energies every 0.2 ps nstlog = 500 ; update log file every 0.2 ps ; Bond parameters continuation = yes ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.5 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = cut-off ; Particle Mesh Ewald for long-range electrostatics ; ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = Protein SOL ; three coupling groups - more accurate tau_t = 0.2 0.2 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 5.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, 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 ; assign velocities from Maxwell distribution ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = system
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