I would be most thankful if you could help me warning 1, note 1 and thr fatal error. I I read about -n option but I dont know where in command line i have to include it. Thank you.
grompp -f pr -c Hexane_b4pr.gro -r Hexane_b4pr.gro -p HexaneModified-Residuename.top -o Hexane_pr >& output.grompp_pr output file: output.grompp_pr *WARNING 1 [file pr.mdp, line unknown]: Unknown or double left-hand 'warnings' in parameter file* checking input for internal consistency... *NOTE 1 [file pr.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat.* Opening library file /chem_soft/gromacs/share/ gromacs/top/ffoplsaa.itp Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'HEX' processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K renumbering atomtypes... converting bonded parameters... NOTE 2 [file HexaneModified-Residuename.top, line unknown]: The largest charge group contains 20 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. initialising group options... processing index file... Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat ------------------------------------------------------- Program grompp, VERSION 4.0.7 Source code file: readir.c, line: 1007 *Fatal error: Group protein not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. * ------------------------------------------------------- pr.mdp file:************************************************************* warnings = 10 cpp = /lib/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 500 ; total 1.0 ps. nstcomm = 1 nstxout = 10 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = protein sol ref_t = 300 300 ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529
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