----- Original Message ----- From: John Shultz <[email protected]> Date: Sunday, June 27, 2010 2:11 Subject: [gmx-users] Bond Energies Absent To: Discussion list for GROMACS users <[email protected]>
> 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> > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search > before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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