In God We Trust Hello Dear GMX users I want to do MD on one peptide in water with gromacs 4.5.3. I minimized and equilibrated my system in NPT and NVT for 50 ps , but when I do final mdrun it has load imbalance and when I try -pd option it stops after 265 ps without any error massage !, can everybody help me. Here is my mdp file . constraints = hbonds integrator = md dt = 0.002 nsteps = 50000000 nstcomm = 10 comm_mode = Linear comm_grps = protein nstxout = 250 nstvout = 1000 nstfout = 0 nstcalcenergy = 10 nstlog = 1000 nstenergy = 1000 nstlist = 10 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb = 1.2 rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes energygrps = protein SOL ; Berendsen temperature coupling is on in three groups Tcoupl = v-rescale tau_t = 0.1 1 tc-grps = protein bulk ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinello-Rahman tau_p = 1 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
Many thanks in advance for your help and your reply. Yours truly Karim Mahnam Institute of Biochemistry and Biophysics (IBB) Tehran University P.O.box 13145-1384 Tehran Iran http://www.ibb.ut.ac.ir/
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