[gmx-users] Bond Energies Absent

[Mark Abraham]

----- Original Message -----
From: John Shultz <jackygrahamez at gmail.com>
Date: Sunday, June 27, 2010 2:11
Subject: [gmx-users] Bond Energies Absent
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> 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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