Dear all
Im trying to extract the interaction energies between protein and solvent. Since PME cant be used for this, plain cutoffs causes problems and shifted cut-offs gives incorrect energies I want to use switched cutoff but with rather long cutoffs to get the correct energy. Unfortunately my system is unstable and within a few ps the total energy and kinetic energy fluctuates several hundred per cent. I´ve tried different options but can´t get it to stabilize except if I´m using any other coulomb type. Any ideas? title = Dyna cpp = /usr/bin/cpp constraints = hbonds integrator = md dt = 0.002 nsteps = 20000000 nstxout = 20000000 nstvout = 20000000 nstfout = 5000 nstlog = 250 nstenergy = 500 nstxtcout = 500 xtc_grps = energygrps = polar hydrophobic peptide SOL nstlist = 1 ns_type = grid coulombtype = switch rcoulomb_switch = 1.4 rcoulomb = 1.7 rlist = 2.0 vdwtype = switch rvdw_switch = 1.4 rvdw = 1.7 tcoupl = nose-hoover tc-grps = Protein Non-Protein tau_t = 0.5 0.5 ref_t = 298 298 Pcoupl = parrinello-rahman tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ;disre_fc = 30 gen_vel = yes gen_temp = 298 gen_seed = 173529 unconstrained_start = no Thanks Matteus --------------------------------------------------------- Matteus Lindgren, graduate student Department of Chemistry, Umeå University SE-901 87 Umeå, Sweden Phone: +46 (0)90-7865368
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