- Original Message -
From: John Shultz
Date: Sunday, June 27, 2010 2:11
Subject: [gmx-users] Bond Energies Absent
To: Discussion list for GROMACS users
> Hi All,>
> My edr files don't contain bond energies. Is there any reason apparent in
> this parameter file?
Since you've constrained all bonds to their equilibrium lengths, what energy
can they have?
Mark
> ntegrator = md> nsteps = 1000> dt = 0.002 > nstvout = 100> nstlog = 500>
> nstenergy = 250> nstxtcout = 100> nstxout = 100> energygrps = Protein_LIG>
> constraints = all-bonds> nstcomm = 1> ns_type = grid > rlist = 1.2> rcoulomb
> = 1.1> rvdw = 1.0> vdwtype = shift> rvdw-switch = 0.9> coulombtype =
> PME-Switch> Tcoupl = v-rescale> ;tau_t = 0.1 0.1> tau_t = 0.1 > tc-grps =
> Protein_LIG> ref_t = 300> Pcoupl = parrinello-rahman> PcOupltype = isotropic>
> tau_p = 0.5> compressibility = 4.5e-5> ref_p = 1.0> gen_vel = yes >
> lincs-iter = 2> DispCorr = EnerPres> optimize_fft = yes> gen_seed = 671928>
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